From 2d93215b3714f726ff6f65ef8897f49d71496a14 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 2 Dec 2020 19:58:04 -0500
Subject: [PATCH 01/83] Edit non-param table, add legacy list

---
 .../01-magnetic-resonance-imaging-data.md     | 56 ++++++++++++-------
 1 file changed, 36 insertions(+), 20 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 7574f34bad..4c5096f94b 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -133,29 +133,28 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     anat/
-        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_part-<label>]_<modality_label>.nii[.gz]
-        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<label>]_defacemask.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_part-<label>]_<suffix>.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<suffix>]_defacemask.nii[.gz]
 ```
 
 Anatomical (structural) data acquired for that participant. Currently supported
-modalities include:
-
-| **Name**           | `modality_label` | **Description**                                                                                                                                   |
-| ------------------ | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- |
-| T1 weighted        | T1w              |                                                                                                                                                   |
-| T2 weighted        | T2w              |                                                                                                                                                   |
-| T1 Rho map         | T1rho            | Quantitative T1rho brain imaging <br> <https://www.ncbi.nlm.nih.gov/pubmed/24474423> <br> <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4346383/> |
-| T1 map             | T1map            | quantitative T1 map                                                                                                                               |
-| T2 map             | T2map            | quantitative T2 map                                                                                                                               |
-| T2\*               | T2star           | High resolution T2\* image                                                                                                                        |
-| FLAIR              | FLAIR            |                                                                                                                                                   |
-| FLASH              | FLASH            |                                                                                                                                                   |
-| Proton density     | PD               |                                                                                                                                                   |
-| Proton density map | PDmap            |                                                                                                                                                   |
-| Combined PD/T2     | PDT2             |                                                                                                                                                   |
-| Inplane T1         | inplaneT1        | T1-weighted anatomical image matched to functional acquisition                                                                                    |
-| Inplane T2         | inplaneT2        | T2-weighted anatomical image matched to functional acquisition                                                                                    |
-| Angiography        | angio            |                                                                                                                                                   |
+non-parametric structural MR images include:
+
+| **Name**                                   | `suffix`         | **Description**                                                                                                                                   |
+| ------------------------------------------ | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- |
+| T1 weighted images                         | T1w              | Structural images with predominant T1 contribution.                                                                                               |
+| T2 weighted images                         | T2w              | Structural images with predominant T2 contribution.                                                                                               |
+| Proton density (PD) weighted images        | PDw              | Structural images with predominant PD contribution.                                                                                               |
+| T2star weighted images                     | T2starw          | Structural images with predominant T2star contribution.                                                                                               |
+| Fluid attenuated inversion recovery images | FLAIR            | Structural images with predominant T2 
+contribution (a.k.a T2-FLAIR), in which signal from fluids (e.g., CSF) is nulled out by adjusting inversion 
+time, coupled with notably long repetition and echo times.                                                  |
+| Inplane T1                                 | inplaneT1        | T1 weighted structural image matched to 
+a functional (task) image.                                                                                  |
+| Inplane T2                                 | inplaneT2        | T2 weighted structural image matched to 
+a functional (task) image.                                                                                  |
+| PD and T2 weighted images                  | PDT2             | PDw and T2w images acquired using a dual 
+echo FSE sequence through view sharing process (Johnson et al. 1994)](https://pubmed.ncbi.nlm.nih.gov/8010268/).                                      |
 
 If the structural images included in the dataset were defaced (to protect
 identity of participants) one MAY provide the binary mask that was used to
@@ -238,6 +237,23 @@ Similarly, the OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec)
 key/value can be used to distinguish
 different reconstruction algorithms (for example ones using motion correction).
 
+### Legacy suffixes (to be deprecated)
+
+Some suffixes that were available in versions of the specification prior to
+1.5.0. have been identified as legacy suffixes. The legacy suffixes generate
+inconsistencies and/or ambiguities with additional suffixes added in version
+1.5.0 and so are therefore not recommended for use in new datasets.
+They are, however, still valid suffixes, to maintain backwards compatibility.
+
+The following suffixes are valid, but SHOULD NOT be used for new BIDS compatible
+datasets (created after version 1.5.0.):
+
+| **Name**           | `modality_label` | **Reason to deprecate**                                                                                                                           |
+| ------------------ | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- |
+| T2\*               | T2star           | Ambiguous, may refer to a parametric image or to a conventional image. **Change:** Replaced by `T2starw` or `T2starmap`.                          |
+| FLASH              | FLASH            | FLASH (Fast-Low-Angle-Shot) is a vendor specific implementation for spoiled  gradient echo acquisition. It is commonly used for rapid anatomical imaging and also for many different qMRI applications. When used for a single file, it does not convey any information about the image contrast. When used in a file collection, it may result in conflicts across filenames of different applications. **Change:** Removed from suffixes|
+| Proton density     | PD               | Ambiguous, may refer to a parametric image or to a conventional image. **Change:** Replaced by `PDw` or `PDmap`.                                  |
+
 ## Task (including resting state) imaging data
 
 Currently supported image contrasts include:

From 042a964f3082e38e18b8ae89c1beb0d18bef675e Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 2 Dec 2020 21:03:39 -0500
Subject: [PATCH 02/83] Add table for parametric maps

---
 .../01-magnetic-resonance-imaging-data.md     | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 4c5096f94b..2bfc36ac2f 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -237,6 +237,31 @@ Similarly, the OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec)
 key/value can be used to distinguish
 different reconstruction algorithms (for example ones using motion correction).
 
+Structural MR images whose intensity is represented in a non-arbitrary scale
+constitute parametric maps. Currently supported parametric maps include:
+
+| **Name**                                     | `suffix`  | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
+|----------------------------------------------|-----------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| Longitudinal relaxation time map             | T1map     | In seconds (s). T1 maps are REQUIRED to use this suffix irrespective of the method they are related to. See [this interactive book on T1 mapping](https://qmrlab.org/t1_book/intro) for further reading on T1-mapping.                                                                                                                                                                                                                                                                                                                                                                  |
+| True transverse relaxation time map          | T2map     | In seconds (s). T2 maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
+| Observed transverse relaxation time map      | T2starmap | In seconds (s). T2-star maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
+| Longitudinal relaxation rate map             | R1map     | In seconds<sup>-1</sup> (1/s). R1 maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
+| True transverse relaxation rate map          | R2map     | In seconds<sup>-1</sup> (1/s). R2 maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
+| Observed transverse relaxation rate map      | R2starmap | In seconds<sup>-1</sup> (1/s). R2-star maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
+| Proton density map                           | PDmap     | In arbitrary units (a.u.). PD maps are REQUIRED to use this suffix irrespective of the method they are related to                                                                                                                                                                                                                                                                                                                                                                           |
+| Magnetization transfer ratio map             | MTRmap    | In percentage (%). MTR maps are REQUIRED to use this suffix irrespective of the method they are related to                                                                                                                                                                                                                                                                                                                                                                           |
+| Magnetization transfer saturation map        | MTsat     | In arbitrary units (a.u.). MTsat maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
+| Homogeneous (flat) T1-weighted MP2RAGE image | UNIT1     | In arbitrary units (a.u.). UNIT1 images are REQUIRED to use this suffix irrespective of the method they are related to. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from from `T1w`.                                                                                                                                                        |
+| T1 in rotating frame (T1 rho) map            | T1rho     | In seconds (s). T1-rho maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
+| Myelin water fraction map                    | MWFmap    | In percentage (%). MWF maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
+| Macromolecular tissue volume (MTV) map       | MTVmap    | In arbitrary units (a.u.). MTV maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
+| Combined PD/T2 map                           | PDT2map   | In arbitrary units (a.u.). Combined PD/T2 maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
+| Quantitative susceptibility map (QSM)        | Chimap    | In parts per million (ppm). QSM allows for determining the underlying magnetic susceptibility of tissue (Chi) ([Wang & Liu, 2014](https://onlinelibrary.wiley.com/doi/10.1002/mrm.25358)). Chi maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
+| RF transmit field map                        | TB1map    | In percent units (p.u.). Radio frequency (RF) transmit field maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
+| RF receive sensitivity map                   | RB1map    | In percent units (p.u.). Radio frequency (RF) receive sensitivity maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
+| Observed signal amplitude (S0) map           | S0map     | In arbitrary units (a.u.). For a multi-echo (typically fMRI) sequence, S0 maps index the baseline signal before exponential (T2-star) signal decay. In other words: the exponential of the intercept for a linear decay model across log-transformed echos. For more information, please see, for example, [the tedana documentation](https://tedana.readthedocs.io/en/latest/approach.html#monoexponential-decay-model-fit). S0 maps are RECOMMENDED to use this suffix if derived from an ME-FMRI dataset. |
+| Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (a.u.). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if derived from qMRI applications (e.g. variable flip angle T1 mapping).                                                                                                                                                                                                                                                                                                                                                                            |
+
 ### Legacy suffixes (to be deprecated)
 
 Some suffixes that were available in versions of the specification prior to

From a1660394243e55437d4ece2322863ff8480fdbb7 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 2 Dec 2020 21:45:15 -0500
Subject: [PATCH 03/83] Add description for parametric maps.

---
 .../01-magnetic-resonance-imaging-data.md            | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 2bfc36ac2f..bb6755b408 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -260,7 +260,17 @@ constitute parametric maps. Currently supported parametric maps include:
 | RF transmit field map                        | TB1map    | In percent units (p.u.). Radio frequency (RF) transmit field maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
 | RF receive sensitivity map                   | RB1map    | In percent units (p.u.). Radio frequency (RF) receive sensitivity maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
 | Observed signal amplitude (S0) map           | S0map     | In arbitrary units (a.u.). For a multi-echo (typically fMRI) sequence, S0 maps index the baseline signal before exponential (T2-star) signal decay. In other words: the exponential of the intercept for a linear decay model across log-transformed echos. For more information, please see, for example, [the tedana documentation](https://tedana.readthedocs.io/en/latest/approach.html#monoexponential-decay-model-fit). S0 maps are RECOMMENDED to use this suffix if derived from an ME-FMRI dataset. |
-| Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (a.u.). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if derived from qMRI applications (e.g. variable flip angle T1 mapping).                                                                                                                                                                                                                                                                                                                                                                            |
+| Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (a.u.). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications (e.g. variable flip angle T1 mapping.                                                                                                                                                                                                                                                                                                                                                                      |
+
+Parametric images listed in the table above are typically generated by
+processing a [file collection](../02-common-principles.html#entity-linked-file-collections).
+Please visit the [file collections appendix](../99-appendices/10-file-collections.html) to see the
+list of suffixes available for quantitative MRI (qMRI) applications associated
+with these maps.
+For any other details on the organization of parametric maps, their
+recommended metadata fields, and the application specific entity or
+metadata requirement levels of [file collections](../99-appendices/10-file-collections.html) that can generate
+them, visit the [qMRI appendix](../99-appendices/11-qmri.html).
 
 ### Legacy suffixes (to be deprecated)
 

From 290417378c364496a36abf47acac1040c68ab943 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 2 Dec 2020 21:49:18 -0500
Subject: [PATCH 04/83] Add templates for file collections

---
 src/99-appendices/10-file-collections.md | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/src/99-appendices/10-file-collections.md b/src/99-appendices/10-file-collections.md
index 10e1555e8e..3cb3e40c10 100644
--- a/src/99-appendices/10-file-collections.md
+++ b/src/99-appendices/10-file-collections.md
@@ -24,6 +24,14 @@ included in this appendix:
 
 ### Anatomy imaging data
 
+Template:
+
+```Text
+sub-<label>/[ses-<label>/]
+    anat/
+        sub-<label>[_ses-<label>][_acq-<label>][_echo-<index>][_flip-<index>][_inv-<index>][_mt-<label>][_part-<label>]_<suffix>.nii[.gz]
+```
+
 | Suffix  | Linking entities      | Application                                | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
 |---------|-----------------------|--------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
 | VFA     | flip                  | Variable flip angle                        | The VFA method involves at least two spoiled gradient echo (SPGR) of steady-state free precession (SSFP) images acquired at different flip angles. Depending on the provided metadata fields and the sequence type, data may be eligible for DESPOT1, DESPOT2 and their variants ([Deoni et al. 2005](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.20314)).                                                                                           |
@@ -37,6 +45,12 @@ included in this appendix:
 
 ### Fieldmap data
 
+```Text
+sub-<label>/[ses-<label>/]
+    fmap/
+        sub-<label>[_ses-<label>][_acq-<label>][_echo-<index>][_flip-<index>][_inv-<index>][_mt-<label>][_part-<label>]_<suffix>.nii[.gz]
+```
+
 | Suffix | Meta-data relevant entity    | Application                        | Description                                                                                                                                                                                                                                                                                                                                                                       |
 | ------ | ---------------------------- | ---------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | TB1DAM | flip                         | Double-angle B1+ mapping           | The double-angle B1<sup>+</sup> method ([Insko and Bolinger 1993](https://www.sciencedirect.com/science/article/abs/pii/S1064185883711332)) is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation flip angles. Common sequence types for this application include spin echo and echo planar imaging. |

From a7e2fdbbedd265999db2944d7d1946c3971dbbee Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 2 Dec 2020 22:17:02 -0500
Subject: [PATCH 05/83] Typo, wording for NumberShots

---
 .../01-magnetic-resonance-imaging-data.md                       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index bb6755b408..10f15cea70 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -62,7 +62,7 @@ that a given scan was collected with the intended coil elements selected
 ### In-Plane Spatial Encoding
 | **Key name**                   | **Requirement level** | **Data type** | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
 |--------------------------------|-----------------------|---------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| NumberShots                    | RECOMMENDED           | [number][]    | The number of RF excitations need to reconstruct a slice or volume. Please mind that this is not the same as Echo Train Length which denotes the number of lines of k-space collected after an excitation.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
+| NumberShots                    | RECOMMENDED           | [number][]    | The number of RF excitations needed to reconstruct a slice or volume (may be referred as partition). Please mind that this is not the same as Echo Train Length which denotes the number of k-space lines collected after excitation in a multi-echo readout.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
 | ParallelReductionFactorInPlane | RECOMMENDED           | [number][]    | The parallel imaging (for instance, GRAPPA) factor. Use the denominator of the fraction of k-space encoded for each slice. For example, 2 means half of k-space is encoded. Corresponds to DICOM Tag 0018, 9069 `Parallel Reduction Factor In-plane`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
 | ParallelAcquisitionTechnique   | RECOMMENDED           | [string][]    | The type of parallel imaging used (for example GRAPPA, SENSE). Corresponds to DICOM Tag 0018, 9078 `Parallel Acquisition Technique`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
 | PartialFourier                 | RECOMMENDED           | [number][]    | The fraction of partial Fourier information collected. Corresponds to DICOM Tag 0018, 9081 `Partial Fourier`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |

From a929009c437cfc788054989892b673a56b2d1a5c Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 2 Dec 2020 22:37:45 -0500
Subject: [PATCH 06/83] Add spoiling metadata

---
 .../01-magnetic-resonance-imaging-data.md                | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 10f15cea70..6a1e0fe935 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -55,9 +55,14 @@ that a given scan was collected with the intended coil elements selected
 | MTState                     | RECOMMENDED                                    | [boolean][]                            | Boolean stating whether the magnetization transfer pulse is applied. Corresponds to DICOM tag (0018, 9020) `Magnetization Transfer`.                                                                                                                                      |
 | MTOffsetFrequency           | RECOMMENDED if the MTstate is `True`.          | [number][]                             | The frequency offset of the magnetization transfer pulse with respect to the central H1 Larmor frequency in Hertz (Hz).                                                                                                                                                   |
 | MTPulseBandwidth            | RECOMMENDED if the MTstate is `True`.          | [number][]                             | The excitation bandwidth of the magnetization transfer pulse in Hertz (Hz).                                                                                                                                                                                               |
-| MTNumberOfPulses            | RECOMMENDED if the MTstate is `True`.          | [number][]                             | The number of magnetization transfer RF pulses applied before the readout.                                                                                                                                                                                                |
+| MTNumberOfPulses            | RECOMMENDED if the MTstate is `True`.          | [number][]                             | The number of magnetization transfer RF pulses applied before the readout.                                                                                                                                                                                         |
 | MTPulseShape                | RECOMMENDED if the MTstate is `True`.          | [string][]                             | Shape of the magnetization transfer RF pulse waveform. Accepted values: `HARD`, `GAUSSIAN`, `GAUSSHANN` (gaussian pulse with Hanning window), `SINC`, `SINCHANN` (sinc pulse with Hanning window), `SINCGAUSS` (sinc pulse with Gaussian window), `FERMI`.                |
-| MTPulseDuration             | RECOMMENDED if the MTstate is `True`.          | [number][]                             | Duration of the magnetization transfer RF pulse in seconds.                                                                                                                                                                                                               |
+| MTPulseDuration             | RECOMMENDED if the MTstate is `True`.          | [number][]                             | Duration of the magnetization transfer RF pulse in seconds.                                                                                                                                                                                          |
+| SpoilingState               | RECOMMENDED                                    | [boolean][]                            | Boolean stating whether the pulse sequence uses any type of spoiling strategy to suppress residual transverse magnetization.                                                                                                                                           |
+| SpoilingType                | RECOMMENDED if the SpoilingState is `True`.    | [string][]                             | Specifies which spoiling method(s) are used by a spoiled sequence. Accepted values: `RF`, `GRADIENT` or `COMBINED`.                                                                                                                                                  |
+| SpoilingRFPhaseIncrement    | RECOMMENDED if the SpoilingType has `RF`.      | [number][]                             | The amount of incrementation described in degrees, which is applied to the phase of the excitation pulse at each TR period for achieving RF spoiling.                                                                                                                        |
+| SpoilingGradientMoment      | RECOMMENDED if the SpoilingType has `GRADIENT`. | [number][]                            | Zeroth moment of the spoiler gradient lobe in millitesla times second per meter (mT.s/m).                                                                                                                                                                                   |
+| SpoilingGradientDuration    | RECOMMENDED if the SpoilingType has `GRADIENT`. | [number][]                            | The duration of the spoiler gradient lobe in seconds. The duration of a trapezoidal lobe is defined as the summation of ramp-up and plateu times.                                                                                                                                                                                            |
 
 ### In-Plane Spatial Encoding
 | **Key name**                   | **Requirement level** | **Data type** | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |

From df24f1491c58480d880fcce443a1c9abf0ba8f21 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 2 Dec 2020 23:16:46 -0500
Subject: [PATCH 07/83] Update entity schema src

---
 src/schema/datatypes/anat.yaml | 30 ++++++++++++++++++++++--------
 1 file changed, 22 insertions(+), 8 deletions(-)

diff --git a/src/schema/datatypes/anat.yaml b/src/schema/datatypes/anat.yaml
index e0b8bad9fb..ad0c0e9dc2 100644
--- a/src/schema/datatypes/anat.yaml
+++ b/src/schema/datatypes/anat.yaml
@@ -3,17 +3,31 @@
 - suffixes:
     - T1w
     - T2w
-    - T1rho
-    - T1map
-    - T2map
-    - T2star
+    - PDw
+    - T2starw
     - FLAIR
-    - FLASH
-    - PD
-    - PDmap
-    - PDT2
     - inplaneT1
     - inplaneT2
+    - PDT2
+    - T1map
+    - T2map
+    - T2starmap
+    - R1map
+    - R2map
+    - R2starmap
+    - PDmap
+    - MTRmap
+    - MTsat
+    - UNIT1
+    - T1rho
+    - MWFmap
+    - MTVmap
+    - PDT2map
+    - Chimap
+    - TB1map
+    - RB1map
+    - S0map
+    - M0map
     - angio
   extensions:
     - .nii.gz

From 7f8fb8e9afed03b8389be1e98e6308512fc79b15 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 2 Dec 2020 23:19:00 -0500
Subject: [PATCH 08/83] split

---
 src/schema/datatypes/anat.yaml | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/src/schema/datatypes/anat.yaml b/src/schema/datatypes/anat.yaml
index ad0c0e9dc2..3392f3b053 100644
--- a/src/schema/datatypes/anat.yaml
+++ b/src/schema/datatypes/anat.yaml
@@ -9,6 +9,21 @@
     - inplaneT1
     - inplaneT2
     - PDT2
+    - angio
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    part: optional
+# Second group
+- suffixes:
     - T1map
     - T2map
     - T2starmap
@@ -28,7 +43,6 @@
     - RB1map
     - S0map
     - M0map
-    - angio
   extensions:
     - .nii.gz
     - .nii
@@ -41,7 +55,7 @@
     ce: optional
     rec: optional
     part: optional
-# Second group
+# Third group
 - suffixes:
     - defacemask
   extensions:

From a2f8bd9eb66119f34628fe4edb243ba0b16b0d7f Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Thu, 3 Dec 2020 11:26:00 -0500
Subject: [PATCH 09/83] Update
 src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
---
 .../01-magnetic-resonance-imaging-data.md                       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 6a1e0fe935..344601e5a7 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -159,7 +159,7 @@ a functional (task) image.
 | Inplane T2                                 | inplaneT2        | T2 weighted structural image matched to 
 a functional (task) image.                                                                                  |
 | PD and T2 weighted images                  | PDT2             | PDw and T2w images acquired using a dual 
-echo FSE sequence through view sharing process (Johnson et al. 1994)](https://pubmed.ncbi.nlm.nih.gov/8010268/).                                      |
+echo FSE sequence through view sharing process ([Johnson et al. 1994](https://pubmed.ncbi.nlm.nih.gov/8010268/)).                                      |
 
 If the structural images included in the dataset were defaced (to protect
 identity of participants) one MAY provide the binary mask that was used to

From 6221e322d8da9841056a81cb00a87cb94b8f14c1 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Thu, 3 Dec 2020 11:37:17 -0500
Subject: [PATCH 10/83] Wording

---
 .../01-magnetic-resonance-imaging-data.md     | 34 +++++++++----------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 344601e5a7..3b2364be3e 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -247,23 +247,23 @@ constitute parametric maps. Currently supported parametric maps include:
 
 | **Name**                                     | `suffix`  | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
 |----------------------------------------------|-----------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| Longitudinal relaxation time map             | T1map     | In seconds (s). T1 maps are REQUIRED to use this suffix irrespective of the method they are related to. See [this interactive book on T1 mapping](https://qmrlab.org/t1_book/intro) for further reading on T1-mapping.                                                                                                                                                                                                                                                                                                                                                                  |
-| True transverse relaxation time map          | T2map     | In seconds (s). T2 maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
-| Observed transverse relaxation time map      | T2starmap | In seconds (s). T2-star maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
-| Longitudinal relaxation rate map             | R1map     | In seconds<sup>-1</sup> (1/s). R1 maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
-| True transverse relaxation rate map          | R2map     | In seconds<sup>-1</sup> (1/s). R2 maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
-| Observed transverse relaxation rate map      | R2starmap | In seconds<sup>-1</sup> (1/s). R2-star maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
-| Proton density map                           | PDmap     | In arbitrary units (a.u.). PD maps are REQUIRED to use this suffix irrespective of the method they are related to                                                                                                                                                                                                                                                                                                                                                                           |
-| Magnetization transfer ratio map             | MTRmap    | In percentage (%). MTR maps are REQUIRED to use this suffix irrespective of the method they are related to                                                                                                                                                                                                                                                                                                                                                                           |
-| Magnetization transfer saturation map        | MTsat     | In arbitrary units (a.u.). MTsat maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
-| Homogeneous (flat) T1-weighted MP2RAGE image | UNIT1     | In arbitrary units (a.u.). UNIT1 images are REQUIRED to use this suffix irrespective of the method they are related to. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from from `T1w`.                                                                                                                                                        |
-| T1 in rotating frame (T1 rho) map            | T1rho     | In seconds (s). T1-rho maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
-| Myelin water fraction map                    | MWFmap    | In percentage (%). MWF maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
-| Macromolecular tissue volume (MTV) map       | MTVmap    | In arbitrary units (a.u.). MTV maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
-| Combined PD/T2 map                           | PDT2map   | In arbitrary units (a.u.). Combined PD/T2 maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
-| Quantitative susceptibility map (QSM)        | Chimap    | In parts per million (ppm). QSM allows for determining the underlying magnetic susceptibility of tissue (Chi) ([Wang & Liu, 2014](https://onlinelibrary.wiley.com/doi/10.1002/mrm.25358)). Chi maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
-| RF transmit field map                        | TB1map    | In percent units (p.u.). Radio frequency (RF) transmit field maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
-| RF receive sensitivity map                   | RB1map    | In percent units (p.u.). Radio frequency (RF) receive sensitivity maps are REQUIRED to use this suffix irrespective of the method they are related to.                                                                                                                                                                                                                                                                                                                                                                          |
+| Longitudinal relaxation time map             | T1map     | In seconds (s). T1 maps are REQUIRED to use this suffix regardless of the method used to generate them. See [this interactive book on T1 mapping](https://qmrlab.org/t1_book/intro) for further reading on T1-mapping.                                                                                                                                                                                                                                                                                                                                                                  |
+| True transverse relaxation time map          | T2map     | In seconds (s). T2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| Observed transverse relaxation time map      | T2starmap | In seconds (s). T2-star maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| Longitudinal relaxation rate map             | R1map     | In seconds<sup>-1</sup> (1/s). R1 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| True transverse relaxation rate map          | R2map     | In seconds<sup>-1</sup> (1/s). R2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| Observed transverse relaxation rate map      | R2starmap | In seconds<sup>-1</sup> (1/s). R2-star maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| Proton density map                           | PDmap     | In arbitrary units (a.u.). PD maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                           |
+| Magnetization transfer ratio map             | MTRmap    | In percentage (%). MTR maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                           |
+| Magnetization transfer saturation map        | MTsat     | In arbitrary units (a.u.). MTsat maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| Homogeneous (flat) T1-weighted MP2RAGE image | UNIT1     | In arbitrary units (a.u.). UNIT1 images are REQUIRED to use this suffix regardless of the method used to generate them. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from from `T1w`.                                                                                                                                                        |
+| T1 in rotating frame (T1 rho) map            | T1rho     | In seconds (s). T1-rho maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| Myelin water fraction map                    | MWFmap    | In percentage (%). MWF maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| Macromolecular tissue volume (MTV) map       | MTVmap    | In arbitrary units (a.u.). MTV maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| Combined PD/T2 map                           | PDT2map   | In arbitrary units (a.u.). Combined PD/T2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| Quantitative susceptibility map (QSM)        | Chimap    | In parts per million (ppm). QSM allows for determining the underlying magnetic susceptibility of tissue (Chi) ([Wang & Liu, 2014](https://onlinelibrary.wiley.com/doi/10.1002/mrm.25358)). Chi maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| RF transmit field map                        | TB1map    | In percent units (p.u.). Radio frequency (RF) transmit field maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| RF receive sensitivity map                   | RB1map    | In percent units (p.u.). Radio frequency (RF) receive sensitivity maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
 | Observed signal amplitude (S0) map           | S0map     | In arbitrary units (a.u.). For a multi-echo (typically fMRI) sequence, S0 maps index the baseline signal before exponential (T2-star) signal decay. In other words: the exponential of the intercept for a linear decay model across log-transformed echos. For more information, please see, for example, [the tedana documentation](https://tedana.readthedocs.io/en/latest/approach.html#monoexponential-decay-model-fit). S0 maps are RECOMMENDED to use this suffix if derived from an ME-FMRI dataset. |
 | Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (a.u.). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications (e.g. variable flip angle T1 mapping.                                                                                                                                                                                                                                                                                                                                                                      |
 

From dd64a38789c5b897c6211b355161995ba683126f Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Thu, 3 Dec 2020 11:40:38 -0500
Subject: [PATCH 11/83] a.u. --> arbitrary

---
 .../01-magnetic-resonance-imaging-data.md          | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 3b2364be3e..02cf5dfbd4 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -253,19 +253,19 @@ constitute parametric maps. Currently supported parametric maps include:
 | Longitudinal relaxation rate map             | R1map     | In seconds<sup>-1</sup> (1/s). R1 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
 | True transverse relaxation rate map          | R2map     | In seconds<sup>-1</sup> (1/s). R2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
 | Observed transverse relaxation rate map      | R2starmap | In seconds<sup>-1</sup> (1/s). R2-star maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
-| Proton density map                           | PDmap     | In arbitrary units (a.u.). PD maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                           |
+| Proton density map                           | PDmap     | In arbitrary units (arbitrary). PD maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                           |
 | Magnetization transfer ratio map             | MTRmap    | In percentage (%). MTR maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                           |
-| Magnetization transfer saturation map        | MTsat     | In arbitrary units (a.u.). MTsat maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
-| Homogeneous (flat) T1-weighted MP2RAGE image | UNIT1     | In arbitrary units (a.u.). UNIT1 images are REQUIRED to use this suffix regardless of the method used to generate them. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from from `T1w`.                                                                                                                                                        |
+| Magnetization transfer saturation map        | MTsat     | In arbitrary units (arbitrary). MTsat maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| Homogeneous (flat) T1-weighted MP2RAGE image | UNIT1     | In arbitrary units (arbitrary). UNIT1 images are REQUIRED to use this suffix regardless of the method used to generate them. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from from `T1w`.                                                                                                                                                        |
 | T1 in rotating frame (T1 rho) map            | T1rho     | In seconds (s). T1-rho maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
 | Myelin water fraction map                    | MWFmap    | In percentage (%). MWF maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
-| Macromolecular tissue volume (MTV) map       | MTVmap    | In arbitrary units (a.u.). MTV maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
-| Combined PD/T2 map                           | PDT2map   | In arbitrary units (a.u.). Combined PD/T2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| Macromolecular tissue volume (MTV) map       | MTVmap    | In arbitrary units (arbitrary). MTV maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| Combined PD/T2 map                           | PDT2map   | In arbitrary units (arbitrary). Combined PD/T2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
 | Quantitative susceptibility map (QSM)        | Chimap    | In parts per million (ppm). QSM allows for determining the underlying magnetic susceptibility of tissue (Chi) ([Wang & Liu, 2014](https://onlinelibrary.wiley.com/doi/10.1002/mrm.25358)). Chi maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
 | RF transmit field map                        | TB1map    | In percent units (p.u.). Radio frequency (RF) transmit field maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
 | RF receive sensitivity map                   | RB1map    | In percent units (p.u.). Radio frequency (RF) receive sensitivity maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
-| Observed signal amplitude (S0) map           | S0map     | In arbitrary units (a.u.). For a multi-echo (typically fMRI) sequence, S0 maps index the baseline signal before exponential (T2-star) signal decay. In other words: the exponential of the intercept for a linear decay model across log-transformed echos. For more information, please see, for example, [the tedana documentation](https://tedana.readthedocs.io/en/latest/approach.html#monoexponential-decay-model-fit). S0 maps are RECOMMENDED to use this suffix if derived from an ME-FMRI dataset. |
-| Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (a.u.). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications (e.g. variable flip angle T1 mapping.                                                                                                                                                                                                                                                                                                                                                                      |
+| Observed signal amplitude (S0) map           | S0map     | In arbitrary units (arbitrary). For a multi-echo (typically fMRI) sequence, S0 maps index the baseline signal before exponential (T2-star) signal decay. In other words: the exponential of the intercept for a linear decay model across log-transformed echos. For more information, please see, for example, [the tedana documentation](https://tedana.readthedocs.io/en/latest/approach.html#monoexponential-decay-model-fit). S0 maps are RECOMMENDED to use this suffix if derived from an ME-FMRI dataset. |
+| Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (arbitrary). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications (e.g. variable flip angle T1 mapping.                                                                                                                                                                                                                                                                                                                                                                      |
 
 Parametric images listed in the table above are typically generated by
 processing a [file collection](../02-common-principles.html#entity-linked-file-collections).

From 51a3597c33c91678cbb642ad2bfb5944de73c972 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Thu, 3 Dec 2020 11:48:34 -0500
Subject: [PATCH 12/83] legacy --> deprecated

---
 .../01-magnetic-resonance-imaging-data.md                 | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 02cf5dfbd4..ae6eda3134 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -277,12 +277,12 @@ recommended metadata fields, and the application specific entity or
 metadata requirement levels of [file collections](../99-appendices/10-file-collections.html) that can generate
 them, visit the [qMRI appendix](../99-appendices/11-qmri.html).
 
-### Legacy suffixes (to be deprecated)
+### Deprecated suffixes
 
 Some suffixes that were available in versions of the specification prior to
-1.5.0. have been identified as legacy suffixes. The legacy suffixes generate
-inconsistencies and/or ambiguities with additional suffixes added in version
-1.5.0 and so are therefore not recommended for use in new datasets.
+1.5.0. have been deprecated. These suffixes generate inconsistencies and/or 
+ambiguities with additional suffixes added in version 1.5.0. Therefore, they
+are not recommended for use in new datasets.
 They are, however, still valid suffixes, to maintain backwards compatibility.
 
 The following suffixes are valid, but SHOULD NOT be used for new BIDS compatible

From 24531497f83b378b6d31b889e0f4de4b3bcfe6a2 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Thu, 3 Dec 2020 11:52:28 -0500
Subject: [PATCH 13/83] mod --> label

---
 .../01-magnetic-resonance-imaging-data.md                       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index ae6eda3134..9d5cb32326 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -139,7 +139,7 @@ Template:
 sub-<label>/[ses-<label>/]
     anat/
         sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_part-<label>]_<suffix>.nii[.gz]
-        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<suffix>]_defacemask.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<label>]_defacemask.nii[.gz]
 ```
 
 Anatomical (structural) data acquired for that participant. Currently supported

From 43d717b03bccb386d2ab58ae82c60ddd4a10b918 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Thu, 3 Dec 2020 13:14:01 -0500
Subject: [PATCH 14/83] ADD explanations about fundamental contrasts

---
 .../01-magnetic-resonance-imaging-data.md        | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 9d5cb32326..c2251154b0 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -147,18 +147,18 @@ non-parametric structural MR images include:
 
 | **Name**                                   | `suffix`         | **Description**                                                                                                                                   |
 | ------------------------------------------ | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- |
-| T1 weighted images                         | T1w              | Structural images with predominant T1 contribution.                                                                                               |
-| T2 weighted images                         | T2w              | Structural images with predominant T2 contribution.                                                                                               |
-| Proton density (PD) weighted images        | PDw              | Structural images with predominant PD contribution.                                                                                               |
-| T2star weighted images                     | T2starw          | Structural images with predominant T2star contribution.                                                                                               |
-| Fluid attenuated inversion recovery images | FLAIR            | Structural images with predominant T2 
+| T1 weighted images                         | T1w              | In arbitrary units (abitrary). The contrast of these images is mainly determined by spatial variations in the longitudinal relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively short repetition and echo times. To achieve this weigthing in gradient-echo images, again, short repetition and echo times are selected; however, at relatively large flip angles. Another common approach to increase T1 weighting in gradient-echo images is to add an inversion preparation block to the beginning of the imaging sequence (e.g. `TurboFLASH` or `MP-RAGE`).                           |
+| T2 weighted images                         | T2w              | In arbitrary units (abitrary). The contrast of these images is mainly determined by spatial variations in the (true) transverse relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively long repetition and echo times. Generally, gradient echo sequences are not the most suitable option for achieving T2 weighting, as their contrast natively depends on T2-star rather than on T2.        |
+| Proton density (PD) weighted images        | PDw              | In arbitrary units (abitrary). The contrast of these images is mainly determined by spatial variations in the spin density (1H) of the imaged specimen. In spin-echo sequences this contrast is achieved at short repetition and long echo times. In a gradient-echo acquisition, PD weighting dominates the contrast at long repetition and short echo times, and at small flip angles.|
+| T2star weighted images                     | T2starw          | In arbitrary units (abitrary). The contrast of these images is mainly determined by spatial variations in the (observed) transverse relaxation time of the imaged specimen. In spin-echo sequences, this effect is negated as the excitation is followed by an inversion pulse. The contrast of gradient-echo images natively depends on T2-star effects. However, for T2-star variation to dominate the image contrast, gradient-echo acquisitions are carried out at long repetition and echo times, and at small flip angles.                                                                                                     |
+| Fluid attenuated inversion recovery images | FLAIR            | In arbitrary units (abitrary). Structural images with predominant T2 
 contribution (a.k.a T2-FLAIR), in which signal from fluids (e.g., CSF) is nulled out by adjusting inversion 
 time, coupled with notably long repetition and echo times.                                                  |
-| Inplane T1                                 | inplaneT1        | T1 weighted structural image matched to 
+| Inplane T1                                 | inplaneT1        | In arbitrary units (abitrary). T1 weighted structural image matched to 
 a functional (task) image.                                                                                  |
-| Inplane T2                                 | inplaneT2        | T2 weighted structural image matched to 
+| Inplane T2                                 | inplaneT2        | In arbitrary units (abitrary). T2 weighted structural image matched to 
 a functional (task) image.                                                                                  |
-| PD and T2 weighted images                  | PDT2             | PDw and T2w images acquired using a dual 
+| PD and T2 weighted images                  | PDT2             | In arbitrary units (abitrary). PDw and T2w images acquired using a dual 
 echo FSE sequence through view sharing process ([Johnson et al. 1994](https://pubmed.ncbi.nlm.nih.gov/8010268/)).                                      |
 
 If the structural images included in the dataset were defaced (to protect

From cae53b77123e41a0e89f359986b3bdb3a7b9d0db Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Thu, 3 Dec 2020 13:24:11 -0500
Subject: [PATCH 15/83] Drop part from qMaps

---
 src/schema/datatypes/anat.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/schema/datatypes/anat.yaml b/src/schema/datatypes/anat.yaml
index 3392f3b053..9357cc168f 100644
--- a/src/schema/datatypes/anat.yaml
+++ b/src/schema/datatypes/anat.yaml
@@ -54,7 +54,6 @@
     acq: optional
     ce: optional
     rec: optional
-    part: optional
 # Third group
 - suffixes:
     - defacemask

From 012f1536651fde02cae274854d2cf9055577ada7 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Thu, 3 Dec 2020 13:44:06 -0500
Subject: [PATCH 16/83] update entity table

---
 src/99-appendices/10-file-collections.md |   4 +-
 src/schema/datatypes/anat.yaml           | 102 +++++++++++++++++++++++
 2 files changed, 104 insertions(+), 2 deletions(-)

diff --git a/src/99-appendices/10-file-collections.md b/src/99-appendices/10-file-collections.md
index 3cb3e40c10..88cb52caf4 100644
--- a/src/99-appendices/10-file-collections.md
+++ b/src/99-appendices/10-file-collections.md
@@ -29,7 +29,7 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     anat/
-        sub-<label>[_ses-<label>][_acq-<label>][_echo-<index>][_flip-<index>][_inv-<index>][_mt-<label>][_part-<label>]_<suffix>.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>][_flip-<index>][_inv-<index>][_mt-<label>][_part-<label>]_<suffix>.nii[.gz]
 ```
 
 | Suffix  | Linking entities      | Application                                | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
@@ -48,7 +48,7 @@ sub-<label>/[ses-<label>/]
 ```Text
 sub-<label>/[ses-<label>/]
     fmap/
-        sub-<label>[_ses-<label>][_acq-<label>][_echo-<index>][_flip-<index>][_inv-<index>][_mt-<label>][_part-<label>]_<suffix>.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>][_flip-<index>][_inv-<index>][_mt-<label>][_part-<label>]_<suffix>.nii[.gz]
 ```
 
 | Suffix | Meta-data relevant entity    | Application                        | Description                                                                                                                                                                                                                                                                                                                                                                       |
diff --git a/src/schema/datatypes/anat.yaml b/src/schema/datatypes/anat.yaml
index 9357cc168f..28e0c00897 100644
--- a/src/schema/datatypes/anat.yaml
+++ b/src/schema/datatypes/anat.yaml
@@ -69,3 +69,105 @@
     ce: optional
     rec: optional
     mod: optional
+# Fourth group
+- suffixes:
+    - MESE
+    - MEGRE
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    echo: required
+    part: optional
+# Fifth group
+- suffixes:
+    - VFA
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    flip: required
+    part: optional
+# Sixth group
+- suffixes:
+    - IRT1
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    inv: required
+    part: optional
+# Seventh group
+- suffixes:
+    - MP2RAGE
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    echo: optional
+    flip: required
+    inv: required
+    part: optional
+# Eighth group
+- suffixes:
+    - MPM
+    - MTS
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    echo: optional
+    flip: required
+    mt: required
+    part: optional
+# Nineth group
+- suffixes:
+    - MTR
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    mt: required
+    part: optional
\ No newline at end of file

From d73b9e7b5ff35d49f11c460f5381c62ee37b4c54 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 3 Dec 2020 13:53:22 -0500
Subject: [PATCH 17/83] STY: Use .md links, fix table formatting

---
 .../01-magnetic-resonance-imaging-data.md     | 69 +++++++++----------
 1 file changed, 32 insertions(+), 37 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index c2251154b0..76c2d2528d 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -151,15 +151,10 @@ non-parametric structural MR images include:
 | T2 weighted images                         | T2w              | In arbitrary units (abitrary). The contrast of these images is mainly determined by spatial variations in the (true) transverse relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively long repetition and echo times. Generally, gradient echo sequences are not the most suitable option for achieving T2 weighting, as their contrast natively depends on T2-star rather than on T2.        |
 | Proton density (PD) weighted images        | PDw              | In arbitrary units (abitrary). The contrast of these images is mainly determined by spatial variations in the spin density (1H) of the imaged specimen. In spin-echo sequences this contrast is achieved at short repetition and long echo times. In a gradient-echo acquisition, PD weighting dominates the contrast at long repetition and short echo times, and at small flip angles.|
 | T2star weighted images                     | T2starw          | In arbitrary units (abitrary). The contrast of these images is mainly determined by spatial variations in the (observed) transverse relaxation time of the imaged specimen. In spin-echo sequences, this effect is negated as the excitation is followed by an inversion pulse. The contrast of gradient-echo images natively depends on T2-star effects. However, for T2-star variation to dominate the image contrast, gradient-echo acquisitions are carried out at long repetition and echo times, and at small flip angles.                                                                                                     |
-| Fluid attenuated inversion recovery images | FLAIR            | In arbitrary units (abitrary). Structural images with predominant T2 
-contribution (a.k.a T2-FLAIR), in which signal from fluids (e.g., CSF) is nulled out by adjusting inversion 
-time, coupled with notably long repetition and echo times.                                                  |
-| Inplane T1                                 | inplaneT1        | In arbitrary units (abitrary). T1 weighted structural image matched to 
-a functional (task) image.                                                                                  |
-| Inplane T2                                 | inplaneT2        | In arbitrary units (abitrary). T2 weighted structural image matched to 
-a functional (task) image.                                                                                  |
-| PD and T2 weighted images                  | PDT2             | In arbitrary units (abitrary). PDw and T2w images acquired using a dual 
-echo FSE sequence through view sharing process ([Johnson et al. 1994](https://pubmed.ncbi.nlm.nih.gov/8010268/)).                                      |
+| Fluid attenuated inversion recovery images | FLAIR            | In arbitrary units (abitrary). Structural images with predominant T2 contribution (a.k.a T2-FLAIR), in which signal from fluids (e.g., CSF) is nulled out by adjusting inversion time, coupled with notably long repetition and echo times.                                                  |
+| Inplane T1                                 | inplaneT1        | In arbitrary units (abitrary). T1 weighted structural image matched to a functional (task) image.                                                                                  |
+| Inplane T2                                 | inplaneT2        | In arbitrary units (abitrary). T2 weighted structural image matched to a functional (task) image.                                                                                  |
+| PD and T2 weighted images                  | PDT2             | In arbitrary units (abitrary). PDw and T2w images acquired using a dual echo FSE sequence through view sharing process ([Johnson et al. 1994](https://pubmed.ncbi.nlm.nih.gov/8010268/)).                                      |
 
 If the structural images included in the dataset were defaced (to protect
 identity of participants) one MAY provide the binary mask that was used to
@@ -245,37 +240,37 @@ different reconstruction algorithms (for example ones using motion correction).
 Structural MR images whose intensity is represented in a non-arbitrary scale
 constitute parametric maps. Currently supported parametric maps include:
 
-| **Name**                                     | `suffix`  | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
-|----------------------------------------------|-----------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| Longitudinal relaxation time map             | T1map     | In seconds (s). T1 maps are REQUIRED to use this suffix regardless of the method used to generate them. See [this interactive book on T1 mapping](https://qmrlab.org/t1_book/intro) for further reading on T1-mapping.                                                                                                                                                                                                                                                                                                                                                                  |
-| True transverse relaxation time map          | T2map     | In seconds (s). T2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
-| Observed transverse relaxation time map      | T2starmap | In seconds (s). T2-star maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
-| Longitudinal relaxation rate map             | R1map     | In seconds<sup>-1</sup> (1/s). R1 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
-| True transverse relaxation rate map          | R2map     | In seconds<sup>-1</sup> (1/s). R2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
-| Observed transverse relaxation rate map      | R2starmap | In seconds<sup>-1</sup> (1/s). R2-star maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
-| Proton density map                           | PDmap     | In arbitrary units (arbitrary). PD maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                           |
-| Magnetization transfer ratio map             | MTRmap    | In percentage (%). MTR maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                           |
-| Magnetization transfer saturation map        | MTsat     | In arbitrary units (arbitrary). MTsat maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| **Name**                                     | `suffix`  | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
+|----------------------------------------------|-----------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| Longitudinal relaxation time map             | T1map     | In seconds (s). T1 maps are REQUIRED to use this suffix regardless of the method used to generate them. See [this interactive book on T1 mapping](https://qmrlab.org/t1_book/intro) for further reading on T1-mapping.                                                                                                                                                                                                                                                                                            |
+| True transverse relaxation time map          | T2map     | In seconds (s). T2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                                           |
+| Observed transverse relaxation time map      | T2starmap | In seconds (s). T2-star maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                                      |
+| Longitudinal relaxation rate map             | R1map     | In seconds<sup>-1</sup> (1/s). R1 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                            |
+| True transverse relaxation rate map          | R2map     | In seconds<sup>-1</sup> (1/s). R2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                            |
+| Observed transverse relaxation rate map      | R2starmap | In seconds<sup>-1</sup> (1/s). R2-star maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                       |
+| Proton density map                           | PDmap     | In arbitrary units (arbitrary). PD maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                           |
+| Magnetization transfer ratio map             | MTRmap    | In percentage (%). MTR maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                                       |
+| Magnetization transfer saturation map        | MTsat     | In arbitrary units (arbitrary). MTsat maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                        |
 | Homogeneous (flat) T1-weighted MP2RAGE image | UNIT1     | In arbitrary units (arbitrary). UNIT1 images are REQUIRED to use this suffix regardless of the method used to generate them. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from from `T1w`.                                                                                                                                                        |
-| T1 in rotating frame (T1 rho) map            | T1rho     | In seconds (s). T1-rho maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
-| Myelin water fraction map                    | MWFmap    | In percentage (%). MWF maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
-| Macromolecular tissue volume (MTV) map       | MTVmap    | In arbitrary units (arbitrary). MTV maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
-| Combined PD/T2 map                           | PDT2map   | In arbitrary units (arbitrary). Combined PD/T2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
-| Quantitative susceptibility map (QSM)        | Chimap    | In parts per million (ppm). QSM allows for determining the underlying magnetic susceptibility of tissue (Chi) ([Wang & Liu, 2014](https://onlinelibrary.wiley.com/doi/10.1002/mrm.25358)). Chi maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
-| RF transmit field map                        | TB1map    | In percent units (p.u.). Radio frequency (RF) transmit field maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
-| RF receive sensitivity map                   | RB1map    | In percent units (p.u.). Radio frequency (RF) receive sensitivity maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                          |
+| T1 in rotating frame (T1 rho) map            | T1rho     | In seconds (s). T1-rho maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                                       |
+| Myelin water fraction map                    | MWFmap    | In percentage (%). MWF maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                                       |
+| Macromolecular tissue volume (MTV) map       | MTVmap    | In arbitrary units (arbitrary). MTV maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                          |
+| Combined PD/T2 map                           | PDT2map   | In arbitrary units (arbitrary). Combined PD/T2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                               |
+| Quantitative susceptibility map (QSM)        | Chimap    | In parts per million (ppm). QSM allows for determining the underlying magnetic susceptibility of tissue (Chi) ([Wang & Liu, 2014](https://onlinelibrary.wiley.com/doi/10.1002/mrm.25358)). Chi maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                               |
+| RF transmit field map                        | TB1map    | In percent units (p.u.). Radio frequency (RF) transmit field maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                 |
+| RF receive sensitivity map                   | RB1map    | In percent units (p.u.). Radio frequency (RF) receive sensitivity maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                            |
 | Observed signal amplitude (S0) map           | S0map     | In arbitrary units (arbitrary). For a multi-echo (typically fMRI) sequence, S0 maps index the baseline signal before exponential (T2-star) signal decay. In other words: the exponential of the intercept for a linear decay model across log-transformed echos. For more information, please see, for example, [the tedana documentation](https://tedana.readthedocs.io/en/latest/approach.html#monoexponential-decay-model-fit). S0 maps are RECOMMENDED to use this suffix if derived from an ME-FMRI dataset. |
-| Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (arbitrary). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications (e.g. variable flip angle T1 mapping.                                                                                                                                                                                                                                                                                                                                                                      |
+| Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (arbitrary). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications (e.g. variable flip angle T1 mapping.                                                                                                                                                                                                                                          |
 
 Parametric images listed in the table above are typically generated by
-processing a [file collection](../02-common-principles.html#entity-linked-file-collections).
-Please visit the [file collections appendix](../99-appendices/10-file-collections.html) to see the
+processing a [file collection](../02-common-principles.md#entity-linked-file-collections).
+Please visit the [file collections appendix](../99-appendices/10-file-collections.md) to see the
 list of suffixes available for quantitative MRI (qMRI) applications associated
 with these maps.
 For any other details on the organization of parametric maps, their
 recommended metadata fields, and the application specific entity or
-metadata requirement levels of [file collections](../99-appendices/10-file-collections.html) that can generate
-them, visit the [qMRI appendix](../99-appendices/11-qmri.html).
+metadata requirement levels of [file collections](../99-appendices/10-file-collections.md) that can generate
+them, visit the [qMRI appendix](../99-appendices/11-qmri.md).
 
 ### Deprecated suffixes
 
@@ -288,11 +283,11 @@ They are, however, still valid suffixes, to maintain backwards compatibility.
 The following suffixes are valid, but SHOULD NOT be used for new BIDS compatible
 datasets (created after version 1.5.0.):
 
-| **Name**           | `modality_label` | **Reason to deprecate**                                                                                                                           |
-| ------------------ | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- |
-| T2\*               | T2star           | Ambiguous, may refer to a parametric image or to a conventional image. **Change:** Replaced by `T2starw` or `T2starmap`.                          |
-| FLASH              | FLASH            | FLASH (Fast-Low-Angle-Shot) is a vendor specific implementation for spoiled  gradient echo acquisition. It is commonly used for rapid anatomical imaging and also for many different qMRI applications. When used for a single file, it does not convey any information about the image contrast. When used in a file collection, it may result in conflicts across filenames of different applications. **Change:** Removed from suffixes|
-| Proton density     | PD               | Ambiguous, may refer to a parametric image or to a conventional image. **Change:** Replaced by `PDw` or `PDmap`.                                  |
+| **Name**           | `modality_label` | **Reason to deprecate**                                                                                                                                                                                                                                                                                                                                                                                                                    |
+| ------------------ | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| T2\*               | T2star           | Ambiguous, may refer to a parametric image or to a conventional image. **Change:** Replaced by `T2starw` or `T2starmap`.                                                                                                                                                                                                                                                                                                                   |
+| FLASH              | FLASH            | FLASH (Fast-Low-Angle-Shot) is a vendor specific implementation for spoiled gradient echo acquisition. It is commonly used for rapid anatomical imaging and also for many different qMRI applications. When used for a single file, it does not convey any information about the image contrast. When used in a file collection, it may result in conflicts across filenames of different applications. **Change:** Removed from suffixes. |
+| Proton density     | PD               | Ambiguous, may refer to a parametric image or to a conventional image. **Change:** Replaced by `PDw` or `PDmap`.                                                                                                                                                                                                                                                                                                                           |
 
 ## Task (including resting state) imaging data
 

From c2ecbf3aaf590361bd93e7b70d63e83c888948dd Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Mon, 7 Dec 2020 14:40:00 -0500
Subject: [PATCH 18/83] Update
 src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 .../01-magnetic-resonance-imaging-data.md                       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 76c2d2528d..87e261400d 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -283,7 +283,7 @@ They are, however, still valid suffixes, to maintain backwards compatibility.
 The following suffixes are valid, but SHOULD NOT be used for new BIDS compatible
 datasets (created after version 1.5.0.):
 
-| **Name**           | `modality_label` | **Reason to deprecate**                                                                                                                                                                                                                                                                                                                                                                                                                    |
+| **Name**           | `suffix` | **Reason to deprecate**                                                                                                                                                                                                                                                                                                                                                                                                                    |
 | ------------------ | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
 | T2\*               | T2star           | Ambiguous, may refer to a parametric image or to a conventional image. **Change:** Replaced by `T2starw` or `T2starmap`.                                                                                                                                                                                                                                                                                                                   |
 | FLASH              | FLASH            | FLASH (Fast-Low-Angle-Shot) is a vendor specific implementation for spoiled gradient echo acquisition. It is commonly used for rapid anatomical imaging and also for many different qMRI applications. When used for a single file, it does not convey any information about the image contrast. When used in a file collection, it may result in conflicts across filenames of different applications. **Change:** Removed from suffixes. |

From d901d5843aee0995aff5e146f59b3c29d7c04416 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Tue, 8 Dec 2020 01:21:17 -0500
Subject: [PATCH 19/83] [ADD] qMRI Appendix

---
 mkdocs.yml                   |   1 +
 src/99-appendices/11-qmri.md | 546 +++++++++++++++++++++++++++++++++++
 2 files changed, 547 insertions(+)
 create mode 100644 src/99-appendices/11-qmri.md

diff --git a/mkdocs.yml b/mkdocs.yml
index 4fce5fb957..5219216eeb 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -50,6 +50,7 @@ nav:
         - Coordinate systems: 99-appendices/08-coordinate-systems.md
         - Entities: 99-appendices/09-entities.md
         - File collections: 99-appendices/10-file-collections.md
+        - Quantitative MRI: 99-appendices/11-qmri.md
       - Changelog: CHANGES.md
     - The BIDS Starter Kit:
       - GitHub repository: https://github.com/bids-standard/bids-starter-kit
diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
new file mode 100644
index 0000000000..d73ede06bb
--- /dev/null
+++ b/src/99-appendices/11-qmri.md
@@ -0,0 +1,546 @@
+# Appendix XI: Quantitative MRI
+
+Quantitative MRI (qMRI) is a collection of methods aiming at generating parametric
+maps that can characterize underlying tissue properties. Unlike that of conventional
+MR images (e.g., `T1w`, `T2w`), intensity values of quantitative maps are not represented
+in an arbitrary grayscale range. Instead, these maps are represented either in absolute 
+physical units (e.g., `seconds` for `T1map`), or within an application dependent range of
+arbitrary units (e.g., myelin water fraction `MWFmap` in brain).
+
+## Organization of qMRI data in BIDS
+
+Unlike conventional MR images, quantitative maps are not immediate products of the
+image reconstruction step (from k-space data to structural images).
+Intensity values of qMRI maps are calculated by fitting a collection of parametrically
+linked images to a biophysical model or to an MRI signal representation. This processing
+is typically carried out in the image domain.
+There are two main ways to obtain a quantitative map:
+
+1. Pre-generated qMRI maps: The qMRI maps are generated right after the reconstruction
+of required input images and made available to the user at the scanner console.
+The acquisition scenarios may include (a) vendor pipelines or (b) open-source pipelines
+deployed at the scanner site.
+
+2. Post-generated qMRI maps: The qMRI maps are generated from a collection of input
+data after they are exported from the scanner site. This type of processing is commonly
+carried out using an open-source software such as [hMRI toolbox](https://github.com/hMRI-group/hMRI-toolbox), [mrQ](https://github.com/mezera/mrQ), [PyQMRI](https://github.com/IMTtugraz/PyQMRI), [qmap](https://www.medphysics.wisc.edu/~samsonov/qmap/doc/qmap.html),
+[qMRLab](https://github.com/qmrlab/qmrlab) and [QUIT](https://github.com/spinicist/QUIT).
+
+### Inputs are file collections
+
+The common concept of [entity-linked file collections](../02-common-principles.md#entity-linked-file-collections) enables the description of a qMRI
+application by creating logical groups of input files through `suffix` and certain entities
+representing acquisition parameters (`echo`, `flip`,`inv`, `mt`) or file parts (`part`).
+
+If a qMRI file collection is intended for creating structural quantitative maps (e.g., `T1map`),
+files belonging to that collection are stored in the `anat` subfolder. Below is an example 
+file collection for `MP2RAGE`: 
+
+```
+└── sub-01/
+     └── anat/
+         ├── sub-01_inv-1_part-mag_MP2RAGE.nii.gz
+         ├── sub-01_inv-1_part-phase_MP2RAGE.nii.gz
+         ├── sub-01_inv-1_MP2RAGE.json
+         ├── sub-01_inv-2_part-mag_MP2RAGE.nii.gz
+         ├── sub-01_inv-2_part-phase_MP2RAGE.nii.gz
+         └── sub-01_inv-2_MP2RAGE.json
+```
+
+Commonly, RF fieldmaps (`B1+` and `B1-` maps) are used for the correction of structural quantitative
+maps. As these images do not convey substantial structural information, respective file collections
+of RF fieldmaps are stored in the `fmap` subfolder. Below is an example file collection for RF transmit
+field map `TB1EPI`:
+
+```
+└── sub-01/
+     └── fmap/
+         ├── sub-01_fa-1_echo-1_TB1EPI.nii.gz
+         ├── sub-01_fa-1_echo-1_TB1EPI.json
+         ├── sub-01_fa-1_echo-2_TB1EPI.nii.gz
+         ├── sub-01_fa-1_echo-2_TB1EPI.json
+         ├── sub-01_fa-2_echo-1_TB1EPI.nii.gz
+         ├── sub-01_fa-2_echo-1_TB1EPI.json
+         ├── sub-01_fa-2_echo-2_TB1EPI.nii.gz
+         └── sub-01_fa-2_echo-2_TB1EPI.json
+```
+
+Please visit the [file collections appendix](../99-appendices/10-file-collections.md#magnetic-resonance-imaging) to see the list of currently supported qMRI applications.
+
+### Quantitative maps are derivatives 
+
+Regardless of how they are obtained (pre- or post-generated), qMRI maps are stored in the
+`derivatives` folder. For example a `T1map` can be generated from an `MP2RAGE` file collection
+using either options. If the map is post-generated:
+
+```
+ ds-example/
+ └── derivatives/
+     └── qMRI-software-name/
+         └── sub-01/
+             └── anat/
+                 ├── sub-01_T1map.nii.gz
+                 ├── sub-01_T1map.json
+                 ├── sub-01_UNIT1.nii.gz
+                 └── sub-01_UNIT1.json
+```
+
+If the map is pre-generated, for example, by a Siemens scanner:
+
+```
+ ds-example/
+ └── derivatives/
+     └── Siemens/
+         └── sub-01/
+             └── anat/
+                 ├── sub-01_T1map.nii.gz
+                 ├── sub-01_T1map.json
+                 ├── sub-01_UNIT1.nii.gz
+                 └── sub-01_UNIT1.json
+```
+
+Note: Even though the process from which pre-generated qMRI maps are obtained (vendor pipelines)
+is not known, vendors generally allow exporting of the corresponding input data. It is
+RECOMMENDED to share them along with the vendor outputs, whenever possible for a qMRI method
+supported by BIDS.
+
+### Example datasets
+
+You can find example file collections and qMRI maps organized according to BIDS at [https://osf.io/k4bs5/](https://osf.io/k4bs5/).
+
+## Metadata requirements for qMRI data
+
+The table of required entities for qMRI file collections are provided in the [entity table](../99-appendices/04-entity-table.md). However,
+viability of a qMRI file collection is determined not only by the naming and organization of the
+input files, but also by which metadata fields are provided in accompanying json files.
+
+### Method-specific priority levels for qMRI file collections
+
+#### Anatomy imaging data
+
+| **File collection**  | **REQUIRED metadata**                                                                                                        | **OPTIONAL metadata**      |
+|----------------------|------------------------------------------------------------------------------------------------------------------------------|----------------------------|
+| VFA                  | `FlipAngle`, `PulseSequenceType`, `RepetitionTimeExcitation`                                                                 | `SpoilingRFPhaseIncrement` |
+| IRT1                 | `InversionTime`                                                                                                              |                            |
+| MP2RAGE<sup>*</sup>  | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreperation`, `NumberShots`,`MagneticFieldStrength` | `EchoTime`                 |
+| MESE                 | `EchoTime`                                                                                                                   |                            |
+| MEGRE                | `EchoTime`                                                                                                                   |                            |
+| MTR                  | `MTState`                                                                                                                    |                            |
+| MTS                  | `FlipAngle`, `MTState`, `RepetitionTimeExcitation`                                                                           |                            |
+| MPM                  | `FlipAngle`, `MTState`, `RepetitionTimeExcitation`                                                                           | `EchoTime`                 |
+
+<sup>*</sup> Please see MP2RAGE-specific notes for the calculation of `NumberShots` and regarding the
+organization of `UNIT1` image.
+
+Explanation of the table:
+
+* The metadata fields listed in the REQUIRED column are needed to perform a minimum viable
+qMRI processing for the corresponding `file collection`.
+* Note that some of the metadata fields may be constant across different files in a file
+collection, yet still required as an input (e.g. `NumberShots` in `MP2AGE`). Such metadata
+fields MUST be provided in the accompanying json files.
+* The metadata fields listed in the OPTIONAL column can be used to form different flavors
+of an existing file collection suffix, despensing with the need for introducing a new
+suffix. See _Deriving the intended qMRI application from an ambiguos file collection_
+section for details.
+
+#### Field maps
+
+| **File collection**     | **REQUIRED metadata**                                                                                |
+|-------------------------|------------------------------------------------------------------------------------------------------|
+| TB1DAM                  | `FlipAngle`                                                                                          |
+| TB1EPI                  | `EchoTime`, `FlipAngle`, `TotalReadoutTime`, `MixingTime`                                            |
+| TB1AFI                  | `RepetitionTime`                                                                                     |
+| TB1TFL                  |                                                                                                      |
+| TB1RMF                  |                                                                                                      |
+| TB1SRGE<sup>*</sup>     | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreperation`, `NumberShots` |
+| RB1COR                  |                                                                                                      |
+
+<sup>*</sup> Please see TB1SRGE-specific notes for the calculation of `NumberShots`.
+
+### Meta-data requirements for qMRI maps
+
+As qMRI maps are stored as derivatives, they are subjected to the metadata requirements of 
+[derived datasets](03-modality-agnostic-files.html#derived-dataset-and-pipeline-description).
+
+An example `dataset_description.json` for a qMRI map derivatives folder: 
+
+```
+ ds-example/
+ └── derivatives/
+     └── qMRLab/
+         ├── dataset_description.json
+         └── sub-01/
+             └── anat/
+                 ├── sub-01_T1map.nii.gz
+                 ├── sub-01_T1map.json
+                 ├── sub-01_M0map.nii.gz
+                 └── sub-01_M0map.json
+```
+
+
+```
+dataset_description.json: 
+{
+  "Name": "qMRLab Outputs",
+  "BIDSVersion": "1.5.0",
+  "DatasetType": "derivative",
+  "GeneratedBy": [
+    {
+      "Name": "qMRLab",
+      "Version": "2.4.1",
+      "Container": {
+        "Type": "docker",
+        "Tag": "qmrlab/minimal:2.4.1"
+        }
+    },
+    {
+      "Name": "Manual",
+      "Description": "Generated example T1map outputs"
+    }
+  ],
+  "SourceDatasets": [
+    {
+      "DOI": "DOI 10.17605/OSF.IO/K4BS5",
+      "URL": "https://osf.io/k4bs5/",
+      "Version": "1"
+    }
+  ]
+}
+```
+
+In addition to the metadata fields provided in the `dataset_description.json`, qMRI maps
+are RECOMMENDED to be accompanied by sidecar JSON files that contain further information
+about the quantified maps. Although this may not be the generic case for common derivative
+outputs, a proper interpretation of qMRI maps may critically depend on some metadata
+fields. For example, without the information of `MagneticFieldStrength`, white-matter T1
+values in a `T1map` become elusive.
+
+* All the acquisition parameters that are constant across the files in a file collection
+are RECOMMENDED to be added to the sidecar json of the qMRI maps.
+* Relevant acquisition parameters that vary across files in a qMRI file collection are
+RECOMMENDED to be added to the sidecar json of the qMRI map **`in array form`**.
+* The JSON file accompanying a qMRI map which is obtained by using open-source software
+is RECOMMENDED to include additional metadata fields listed in the following table:
+
+| **Field name**                  | **Definition**                                                                                                               |
+| ------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- |
+| `BasedOn`                       | List of files in a file collection to generate the map. Fieldmaps are also listed, if involved in the processing.            |
+| `EstimationReference`           | Reference to the study/studies on which the implementation is based.                                                         |
+| `EstimationAlgorithm`           | Type of algoritm used to perform fitting (e.g. linear, non-linear, LM etc.)                                                  |
+| `Units`                         | Units of the maps, in accordance with the BIDS specification.                                                                |
+
+Example:
+
+```Text
+sub-01_T1map.nii.gz
+sub-01_T1map.json
+```
+
+```
+sub-01_T1map.json
+{
+
+<<Parameter injected by the software/pipeline>>
+
+"BasedOn":["anat/sub-01_fa-1_VFA.nii.gz",
+           "anat/sub-01_fa-2_VFA.nii.gz",
+           "anat/sub-01_fa-3_VFA.nii.gz",
+           "anat/sub-01_fa-4_VFA.nii.gz",
+           "fmap/sub-01_TB1map.nii.gz"],
+"EstimationPaper":"Deoni et. al.MRM, 2015",
+"EstimationAlgorithm":"Linear",
+"Units": "second",
+
+<<Parameters that are constant across files in the (parent) file collection>>
+
+“MagneticFieldStrength”: “3”,
+“Manufacturer”: “Siemens”,
+“ManufacturerModelName”: “TrioTim”,
+“InstitutionName”: “xxx”,
+“PulseSequenceType”: “SPGR”,
+“PulseSequenceDetails”: “Information beyond the sequence type that identifies
+ specific pulse sequence used (VB version, if not standard, Siemens WIP XXX
+ ersion ### sequence written by xx using a version compiled on mm/dd/yyyy/)”,
+"RepetitionTimeExcitation": "35",
+"EchoTime": "2.86",
+"SliceThickness": "5",
+
+<<Relevant parameters that vary across the linking entity of the (parent) file collection>>
+
+"FlipAngle": ["5","10","15","20"]
+
+}
+```
+
+## Deriving the intended qMRI application from an ambiguous file collection
+
+Certain file colleciton suffixes may refer to a generic data collection regime such 
+as variable flip angle (VFA), rather than a more specific acquisition, e.g.,
+magnetization prepared two gradient echoes (MP2RAGE). Such generic acquisitions
+can serve as a basis to derive various qMRI applications by changes to the acquisition
+sequence (e.g. readout) type or by varying additional scan parameters.
+
+If such an inheritance relationship is applicable between an already existing file
+collection and a new qMRI application to be included in the specification, the inheritor
+qMRI method is listed in the table below instead of introducing a new file collection suffix.
+This approach aims at:
+
+* preventing the list of available suffixes from over-proliferation,
+* providing qMRI-focused BIDS applications with a set of meta-data driven rules to infer 
+possible fitting options,
+* keeping an inheritance track of the qMRI methods described within the specification.
+
+| **File-collection suffix** | **If REQUIRED metadata == Value** | **OPTIONAL metadata [`entity`/`fixed`]**   | **Derived application name (NOT a suffix)** |
+|----------------------------|-----------------------------------|--------------------------------------------|---------------------------------------------|
+| VFA                        | `PulseSequenceType` == `SPGR`     |                                            | DESPOT1                                     |
+| VFA                        | `PulseSequenceType` == `SSFP`     | `SpoilingRFPhaseIncrement` [`fixed`]       | DESPOT2                                     |
+| MP2RAGE                    |                                   | `EchoTime` [`echo`]                        | MP2RAGE-ME                                  |
+| MPM                        |                                   | `EchoTime` [`echo`]                        | MPM-ME                                      |
+
+<sup>*</sup> [`entity`/`fixed`] denotes whether the OPTIONAL metadata that forms a new
+flavor of qMRI applicaiton for the respective suffix varies across files of a file colleciton
+(which calls for using a linking entity) or fixed. If former is the case, the entity is to be
+added to the files in that file collection. Note that this addition MUST be allowed by the
+priority levels given for that suffix in the [`entity table`](../99-appendices/04-entity-table.md). If latter (`fixed`) is the case,
+filenames will remain the same; however, the optional metadata (third column) may
+define the flavor of the application (fourth column) along with the conditional value of a
+required metadata field (second column).
+
+A derived qMRI application becomes avaiable if all the optional metadata fields
+listed for the respective file collection suffix is provided for the data. In addition,
+conditional rules based on the value of a given required metada field can be set
+for the description of a derived qMRI application. Note that the value of this
+required metadata is fixed across constituent images of a file collection and defined
+in the _Method-specific priority levels for qMRI file collections_ section above.
+
+For example, if the optional metadata field of `PulseSequenceType` is SPGR
+for a collection of anatomical images listed by the `VFA` suffix, the data
+qualifies for `DESPOT1` T1 fitting. For the same suffix, if the `PulseSequenceType`
+metadata field has the value of `SSFP`, and the `SpoilingRFPhaseIncrement` is 
+provided as a metadata field, then the dataset becomes eligible for `DESPOT2`
+T2 fitting application.
+
+Please note that optional metadata fields listed in the _Deriving the intended qMRI_
+_application from an ambiguous file collection_ table are included in the optional (third)
+column of the _Method-specific priority levels for qMRI file collections_ table for
+the consistency of this appendix.
+
+## Introducing a new qMRI file collection
+
+If a qMRI application can not be interpreted as subset of an already existing suffix
+of a qMRI-related file collection, we RECOMMEND adhering to the following principles to 
+introduce a new suffix:
+
+* All qMRI-relevant file collection suffixes are capitalized.
+* Unless the pulse sequence is exclusively associated with a specific qMRI application
+(e.g. `MP2RAGE`), sequence names are not used as suffixes.
+* File collection suffixes for qMRI applications attain a clear description
+of the qMRI method that they relate to in the [file collections appendix]((../99-appendices/10-file-collections.md#magnetic-resonance-imaging)).
+Hyperlinks to example applications and reference method articles are encouraged
+whenever possible.
+* If it is possible to derive a qMRI application from an already existing file collection
+suffix by defining a set of logical conditions over the metadata fields, the tables of
+_Deriving the intended qMRI application from an ambiguous file collection_ and the
+_Method-specific priority levels for qMRI file collections/Anatomy_ sections are extended 
+instead of introducing a new suffix.
+
+## Application-specific notes for qMRI file collections
+
+### Anatomy imaging data
+
+General notes:
+
+* Some BIDS metadata field values are calculated based on the values of other metadata fields
+that are not listed as required fields. These fields include: `NumberShots`. The calculation of
+the values may depend on the type of the acquisition. These acquisitions include: `MP2RAGE` and 
+`TB1SRGE`. 
+
+#### `MP2RAGE` specific notes
+
+##### `UNIT1` images
+
+Although the `UNIT1` image is provided as an output by the acquisition sequence, it is used
+as an input to offline calculation of a `T1map` using a dictionary lookup approach. However,
+`complex` data is needed for an accurate calculation of the `UNIT1` image, which is not commonly
+provided by the stock sequence. Instead, the `magnitude` and `phase` images are exported. Please
+see the relevant discussion [here](https://github.com/qMRLab/qMRLab/issues/255).
+
+Therefore, the `UNIT1` image provided by the scanner is RECOMMENDED to be stored under the `anat`
+raw dataset directory along with the `MP2RAGE` file collection and to be used as the primary input
+for quantifying a `T1map`. 
+
+If an additional `UNIT1` image is calculated offline, then the output is to be stored in the 
+`derivatives` folder with neccesary provenance information.
+
+##### `NumberShots` metadata field 
+
+Note that type of `NumberShots` field can be either a `number` or an `array of numbers`.
+
+* If a single `number` is to be provided, this should correspond to the number of `SlicesPerSlab` or 
+`ReconMatrixPE`. However, in this case, `SlicePartialFourier` or `PartialFourierPE` fraction is needed
+to calculate the number of partitions `before` and `after` of the k-space center to calculate a T1 map.
+* If `before/after` calculation is performed during the BIDS conversion of the `MP2RAGE` data, then
+then the value of `NumberShots` metadata field can be given as a 1X2 array, with first entry corresponding
+to `before` and the second to the `after`.
+
+Formula:
+
+If NumberShots is an array of numbers such that `"NumberShots": [before, after]`, the values of
+`before` and `after` are calculated as follows ([reference](https://github.com/JosePMarques/MP2RAGE-related-scripts/blob/a405df30ac2c617d29d8b1b16025aaa911e86370/func/bids_T1B1correct.m#L16)):
+
+```
+before = SlicesPerSlab*(SlicePartialFourier - 0.5)
+after  = SlicesPerSlab/2
+```
+
+##### Other metadata fields
+
+The value of the `RepetitionTimeExcitation` is not commonly found in the DICOM files. When
+accessible, the value of `EchoSpacing` corresponds to this metadata. When not accessible,
+`2 X EchoTime` can be used as a surrogate.
+
+Further information about other `MP2RAGE` qMRI protocol fields can be found [here](https://qmrlab.readthedocs.io/en/master/protocols.html#mp2rage).
+
+#### `TB1SRGE` specific notes
+
+Calculation of `before` and `after` entries for `NumberShots` metadata field of `TB1SRGE`
+is more involved than that of `MP2RAGE`. The formula can be found [here](https://github.com/JosePMarques/MP2RAGE-related-scripts/blob/a405df30ac2c617d29d8b1b16025aaa911e86370/DemoForR1Correction.m#L17), which requires 
+information about `BaseResolution` (i.e. image matrix size in PE direction), partial Fourier
+fraction in the PE direction, number of reference lines for parallel imaging acceleration
+and the parallel imaging acceleration factor in PE direction.
+
+
+### Radiofrequency (RF) field mapping
+
+General note:
+
+Some RF file collections call for the use of special notations that cannot be resolved by
+by entities that can generalize to other applications. Instead of introducing an entity
+that is exclusive to a single application, method developers who commonly use these file
+collections for the `MPM` application reached the consensus on the use of `acq` entity to
+distinguish individual files. These suffixes include: `TB1AFI`, `TB1TFL`, `TB1RMF` and
+`RB1COR`.
+
+#### `TB1EPI` specific notes
+
+The `flip` and `echo` entities MUST be used to distinguish images with this suffix.
+The use of `flip` follows the default convention. However, this suffix defines a
+specific use case for the `echo` entity:
+
+|`echo-1`|`echo-2`|
+|:--|:----|
+|Lower `EchoTime` | Higher `EchoTime`                  |
+|Spin Echo (SE) image|Stimulated Echo (STE) image|
+
+At each `FlipAngle`, the `TB1EPI` suffix lists two images acquired at two echo times.
+The first echo is a spin echo (SE) formed by the pulses alpha-2alpha. However, the 
+second echo in this method is generated in a different fashion compared to a typical
+MESE acquisition. The second echo is a stimulated echo (STE) that is formed by an 
+additional alpha pulse (i.e., alpha-2alpha-alpha).
+
+The `FlipAngle` value corresponds to the nominal flip angle value of the STE pulse.
+The nominal FA value of the SE pulse is twice this value.
+
+Note that the following metadata fields MUST be defined in the accompanying JSON 
+files:
+
+| Field name         | Definition |
+| :----------------- | :--------- |
+| `TotalReadoutTime` |   The effective readout length defined as `EffectiveEchoSpacing * PEReconMatrix`, with `EffectiveEchoSpacing = TrueEchoSpacing / PEacceleration`         |
+| `MixingTime`       |  Time interval between the SE and STE pulses          |
+
+To properly identify constituents of this particular method, values of the `echo`
+entity MUST index the images as follows:  
+
+```
+└── sub-01/
+     └── fmap/
+         ├── sub-01_echo-1_flip-1_TB1EPI.nii.gz (SE)
+         ├── sub-01_echo-1_flip-1_TB1EPI.json
+         ├── sub-01_echo-2_flip-1_TB1EPI.nii.gz (STE)
+         ├── sub-01_echo-2_flip-1_TB1EPI.json
+         ├── sub-01_echo-1_flip-2_TB1EPI.nii.gz (SE)
+         ├── sub-01_echo-1_flip_2_TB1EPI.json
+         ├── sub-01_echo-2_flip-2_TB1EPI.nii.gz (STE)
+         └── sub-01_echo-2_flip-2_TB1EPI.json
+```
+
+#### `TB1AFI` specific notes
+
+This method calculates a B1<sup>+</sup> map from two images acquired at two
+interleaved excitation repetition times (TR). Note that there is not an entity 
+for the TR and its definition depends on the modality (`functional` or `anatomical`)
+in the specification. 
+
+Therefore, to properly identify constituents of this particular method, values of 
+the `acq` entity SHOULD begin with either `tr1` (lower TR) or `tr2` (higher TR) 
+and MAY be followed by freeform entries:  
+
+|First `TR`|Second `TR`|Use case|
+|:--|:----| :----| 
+|`_acq-tr1`|`_acq-tr2`|Single acquisition|
+|`_acq-tr1Test`|`_acq-tr2Test`|Acquisition `Test`|
+|`_acq-tr1Retest`|`_acq-tr2Retest`|Acquisition `Retest`|
+
+```
+└── sub-01/
+     └── fmap/
+         ├── sub-01_acq-tr1_TB1AFI.nii.gz
+         ├── sub-01_acq-tr1_TB1AFI.json
+         ├── sub-01_acq-tr2_TB1AFI.nii.gz
+         └── sub-01_acq-tr2_TB1AFI.json
+```
+
+#### `TB1TFL` and `TB1RMF` specific notes
+
+These suffixes describe two outputs generated by Siemens `tfl_b1_map` and `rf_map`
+product sequences, respectively. Both sequences output two images. The first image
+appears like an anatomical image and the second output is a scaled flip angle map.
+
+To properly identify files of this particular file collection, values of 
+the `acq` entity SHOULD begin with either `anat` or `famp` and MAY be followed 
+by freeform entries:
+
+|Anatomical (like) image|Scaled FA map|Use case|
+|:--|:----| :----| 
+|`_acq-anat`|`_acq-famp`|Single acquisition|
+|`_acq-anatTest`|`_acq-fampTest`|Acquisition `Test`|
+|`_acq-anatRetest`|`_acq-fampRetest`|Acquisition `Retest`|
+
+```
+└── sub-01/
+     └── fmap/
+         ├── sub-01_acq-anat_TB1TFL.nii.gz 
+         ├── sub-01_acq-anat_TB1TFL.json
+         ├── sub-01_acq-famp_TB1TFL.nii.gz
+         └── sub-01_acq-famp_TB1TFL.json
+```
+
+The example above applies to the `TB1RFM` suffix as well. 
+
+#### `RB1COR` specific notes
+
+This method generates a sensitivity map by combining two low resolution images
+collected by two transmit coils (the body and the head coil) upon subsequent scans
+with identical acquisition parameters.
+
+To properly identify constituents of this particular method, values of the `acq`
+entity SHOULD begin with either `body` or `head` and MAY be followed by freeform
+entries:  
+
+|Body coil|Head coil|Use case|
+|:--|:----| :----| 
+|`_acq-body`|`_acq-head`|Single acquisition|
+|`_acq-bodyMTw`|`_acq-headMTw`|`MTw` for `MPM`|
+|`_acq-bodyPDw`|`_acq-headPDw`|`PDw` for `MPM`|
+|`_acq-bodyT1w`|`_acq-headT1w`|`T1w` for `MPM`|
+
+```
+└── sub-01/
+     └── fmap/
+         ├── sub-01_acq-body_RB1COR.nii.gz (Body coil)
+         ├── sub-01_acq-body_RB1COR.json
+         ├── sub-01_acq-head_RB1COR.nii.gz (Head coil)
+         └── sub-01_acq-head_RB1COR.json
+```
\ No newline at end of file

From 81c2146658fc015224ddae37d903c7b119459e10 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Tue, 8 Dec 2020 01:21:57 -0500
Subject: [PATCH 20/83] ADD SA2RAGE and qMRI appendix links

---
 src/99-appendices/10-file-collections.md | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/src/99-appendices/10-file-collections.md b/src/99-appendices/10-file-collections.md
index 88cb52caf4..986dfc399e 100644
--- a/src/99-appendices/10-file-collections.md
+++ b/src/99-appendices/10-file-collections.md
@@ -36,7 +36,7 @@ sub-<label>/[ses-<label>/]
 |---------|-----------------------|--------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
 | VFA     | flip                  | Variable flip angle                        | The VFA method involves at least two spoiled gradient echo (SPGR) of steady-state free precession (SSFP) images acquired at different flip angles. Depending on the provided metadata fields and the sequence type, data may be eligible for DESPOT1, DESPOT2 and their variants ([Deoni et al. 2005](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.20314)).                                                                                           |
 | IRT1    | inv, part             | Inversion recovery T1 mapping              | The IRT1 method involves multiple inversion recovery spin-echo images acquired at different inversion times ([Barral et al. 2010](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.22497)).                                                                                                                                                                                                                                                               |
-| MP2RAGE | flip, inv, echo, part | Magnetization prepared two gradient echoes | The MP2RAGE method is a special protocol that collects several images at different flip angles and inversion times to create a parametric T1map by combining the magnitude and phase images ([Marques et al. 2010](https://www.sciencedirect.com/science/article/pii/S1053811909010738?casa_token=u_CYBx4hi7IAAAAA:3w0cMTyU5jA1BdFs0s5oVcQeqF2tZho0iJ9d4N1kExfaX27v9-JnWacF6mbEp_lMKZ64CvoTl8k)                                                               |
+| MP2RAGE | flip, inv, echo, part | Magnetization prepared two gradient echoes | The MP2RAGE method is a special protocol that collects several images at different flip angles and inversion times to create a parametric T1map by combining the magnitude and phase images ([Marques et al. 2010](https://www.sciencedirect.com/science/article/pii/S1053811909010738?casa_token=u_CYBx4hi7IAAAAA:3w0cMTyU5jA1BdFs0s5oVcQeqF2tZho0iJ9d4N1kExfaX27v9-JnWacF6mbEp_lMKZ64CvoTl8k)).                                                               |
 | MESE    | echo                  | Multi-echo spin-echo                       | The MESE method involves multiple spin echo images acquired at different echo times and is primarily used for T2 mapping. Please note that this suffix is not intended for the logical grouping of images acquired using an Echo Planar Imaging (EPI) readout.                                                                                                                                                                                                |
 | MEGRE   | echo                  | Multi-echo gradient-echo                   | Anatomical gradient echo images acquired at different echo times. Please note that this suffix is not intended for the logical grouping of images acquired using an Echo Planar Imaging (EPI) readout.                                                                                                                                                                                                                                                        |
 | MTR     | mt                    | Magnetization transfer ratio               | This method is to calculate a semi-quantitative magnetization transfer ratio map.                                                                                                                                                                                                                                                                                                                                                                             |
@@ -51,11 +51,12 @@ sub-<label>/[ses-<label>/]
         sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>][_flip-<index>][_inv-<index>][_mt-<label>][_part-<label>]_<suffix>.nii[.gz]
 ```
 
-| Suffix | Meta-data relevant entity    | Application                        | Description                                                                                                                                                                                                                                                                                                                                                                       |
-| ------ | ---------------------------- | ---------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| TB1DAM | flip                         | Double-angle B1+ mapping           | The double-angle B1<sup>+</sup> method ([Insko and Bolinger 1993](https://www.sciencedirect.com/science/article/abs/pii/S1064185883711332)) is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation flip angles. Common sequence types for this application include spin echo and echo planar imaging. |
-| TB1EPI | flip, echo                   | B1<sup>+</sup> mapping with 3D EPI | This B1<sup>+</sup> mapping method ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)) is based on two EPI readouts to acquire spin echo (SE) and stimulated echo (STE) images at multiple flip angles in one sequence, used in the calculation of deviations from the nominal flip angle.                                                                              |
-| TB1AFI | flip, inv                    | Actual Flip Angle Imaging (AFI)    | This method ([Yarnykh 2007](https://dx.doi.org/10.1002/mrm.21120)) calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence                                                                                                                                                                       |
-| TB1TFL | Please see the qMRI appendix | Siemens `tfl_b1_map`               | B1<sup>+</sup> data acquired using `tfl_b1_map` product sequence by Siemens based on the method by [Chung et al. (2010)](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.22423). The sequence generates one ~anatomical image and one scaled flip angle map.                                                                                                                 |
-| TB1RMF | Please see the qMRI appendix | Siemens `rf_map`                   | B1<sup>+</sup> data acquired using `rf_map` product sequence by Siemens                                                                                                                                                                                                                                                                                                           |
-| RB1COR | Please see the qMRI appendix | B1<sup>-</sup> field correction    | Low resolution images acquired by the body coil (in the gantry of the scanner) and the head coil using identical acquisition parameters to generate a combined sensitivity map as described in [Papp et al. (2016)](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.26058)                                                                                                   |
+| Suffix  | Meta-data relevant entity                                    | Application                        | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+|---------|--------------------------------------------------------------|------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| TB1DAM  | flip                                                         | Double-angle B1+ mapping           | The double-angle B1<sup>+</sup> method ([Insko and Bolinger 1993](https://www.sciencedirect.com/science/article/abs/pii/S1064185883711332)) is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation flip angles. Common sequence types for this application include spin echo and echo planar imaging.                                                                                                |
+| TB1EPI  | flip, echo                                                   | B1<sup>+</sup> mapping with 3D EPI | This B1<sup>+</sup> mapping method ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)) is based on two EPI readouts to acquire spin echo (SE) and stimulated echo (STE) images at multiple flip angles in one sequence, used in the calculation of deviations from the nominal flip angle.                                                                                                                                                                             |
+| TB1AFI  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Actual Flip Angle Imaging (AFI)    | This method ([Yarnykh 2007](https://dx.doi.org/10.1002/mrm.21120)) calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence                                                                                                                                                                                                                                                                      |
+| TB1TFL  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `tfl_b1_map`               | B1<sup>+</sup> data acquired using `tfl_b1_map` product sequence by Siemens based on the method by [Chung et al. (2010)](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.22423). The sequence generates one ~anatomical image and one scaled flip angle map.                                                                                                                                                                                                                |
+| TB1RMF  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `rf_map`                   | B1<sup>+</sup> data acquired using `rf_map` product sequence by Siemens                                                                                                                                                                                                                                                                                                                                                                                                          |
+| TB1SRGE | `flip`, `inv`                                                | SA2RAGE                            | Saturation-prepared with 2 rapid gradient echoes (SA2RAGE) uses a ratio of two saturation recovery images with different time delays, and a simulated look-up table to estimate B1+ ([Eggenschwiler et al. 2011](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.23145)). This sequence can also be used in conjunction with MP2RAGE T1 mapping to iteratively improve B1+ and T1 map estimation ([Marques & Gruetter 2013](https://doi.org/10.1371/journal.pone.0069294)). |
+| RB1COR  | Please see the [qMRI appendix](../99-appendices/11-qmri.md)  | B1<sup>-</sup> field correction    | Low resolution images acquired by the body coil (in the gantry of the scanner) and the head coil using identical acquisition parameters to generate a combined sensitivity map as described in [Papp et al. (2016)](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.26058)                                                                                                                                                                                                  |

From 1d8db2b638c563f2f9eceb10bffb35f154235429 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Tue, 8 Dec 2020 01:27:43 -0500
Subject: [PATCH 21/83] Entity and entity tables

- Avoid conflict with #692
- Add applicable TB1map file collections
---
 src/99-appendices/09-entities.md |  9 +++++++--
 src/schema/datatypes/fmap.yaml   | 33 ++++++++++++++++++++++++++++++++
 2 files changed, 40 insertions(+), 2 deletions(-)

diff --git a/src/99-appendices/09-entities.md b/src/99-appendices/09-entities.md
index 2bbd081438..38ee57d17b 100644
--- a/src/99-appendices/09-entities.md
+++ b/src/99-appendices/09-entities.md
@@ -2,10 +2,15 @@
   This file is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
   Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#updating-the-schema
 -->
-# Appendix IX: Entities
+# Appendix IV: Entity table
 
 This section compiles the entities (key-value pairs) described throughout this
-specification, and describes each.
+specification, and establishes a common order within a filename. 
+For example, if a file has an acquisition and reconstruction label, the
+acquisition entity must precede the reconstruction entity.
+REQUIRED and OPTIONAL entities for a given file type are denoted.
+Entity formats indicate whether the value is alphanumeric
+(`<label>`) or numeric (`<index>`).
 
 A general introduction to entities is given in the section on
 [file name structure](../02-common-principles.md#file-name-structure).
diff --git a/src/schema/datatypes/fmap.yaml b/src/schema/datatypes/fmap.yaml
index 98d0f6c45c..0391a6e0f1 100644
--- a/src/schema/datatypes/fmap.yaml
+++ b/src/schema/datatypes/fmap.yaml
@@ -31,3 +31,36 @@
     ce: optional
     dir: required
     run: optional
+# Third group
+- suffixes:
+    - TB1DAM
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    flip: required
+    part: optional
+# Fourth group
+- suffixes:
+    - TB1EPI
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    echo: required
+    flip: required
+    part: optional

From d838d263b5b731f741f744a7db115eb563eaa019 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Tue, 8 Dec 2020 01:29:08 -0500
Subject: [PATCH 22/83] ADD MixingTime & Improve NumberShots

---
 .../01-magnetic-resonance-imaging-data.md                      | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 87e261400d..444d64199b 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -67,7 +67,7 @@ that a given scan was collected with the intended coil elements selected
 ### In-Plane Spatial Encoding
 | **Key name**                   | **Requirement level** | **Data type** | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
 |--------------------------------|-----------------------|---------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| NumberShots                    | RECOMMENDED           | [number][]    | The number of RF excitations needed to reconstruct a slice or volume (may be referred as partition). Please mind that this is not the same as Echo Train Length which denotes the number of k-space lines collected after excitation in a multi-echo readout.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
+| NumberShots                    | RECOMMENDED           | [number][] or [array][] of [numbers]    | The number of RF excitations needed to reconstruct a slice or volume (may be referred as partition). Please mind that this is not the same as Echo Train Length which denotes the number of k-space lines collected after excitation in a multi-echo readout.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
 | ParallelReductionFactorInPlane | RECOMMENDED           | [number][]    | The parallel imaging (for instance, GRAPPA) factor. Use the denominator of the fraction of k-space encoded for each slice. For example, 2 means half of k-space is encoded. Corresponds to DICOM Tag 0018, 9069 `Parallel Reduction Factor In-plane`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
 | ParallelAcquisitionTechnique   | RECOMMENDED           | [string][]    | The type of parallel imaging used (for example GRAPPA, SENSE). Corresponds to DICOM Tag 0018, 9078 `Parallel Acquisition Technique`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
 | PartialFourier                 | RECOMMENDED           | [number][]    | The fraction of partial Fourier information collected. Corresponds to DICOM Tag 0018, 9081 `Partial Fourier`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
@@ -75,6 +75,7 @@ that a given scan was collected with the intended coil elements selected
 | PhaseEncodingDirection         | RECOMMENDED           | [string][]    | Possible values: `i`, `j`, `k`, `i-`, `j-`, `k-`. The letters `i`, `j`, `k` correspond to the first, second and third axis of the data in the NIFTI file. The polarity of the phase encoding is assumed to go from zero index to maximum index unless `-` sign is present (then the order is reversed - starting from the highest index instead of zero). `PhaseEncodingDirection` is defined as the direction along which phase is was modulated which may result in visible distortions. Note that this is not the same as the DICOM term `InPlanePhaseEncodingDirection` which can have `ROW` or `COL` values. This parameter is REQUIRED if corresponding fieldmap data is present or when using multiple runs with different phase encoding directions (which can be later used for field inhomogeneity correction). |
 | EffectiveEchoSpacing           | RECOMMENDED           | [number][]    | The "effective" sampling interval, specified in seconds, between lines in the phase-encoding direction, defined based on the size of the reconstructed image in the phase direction. It is frequently, but incorrectly, referred to as "dwell time" (see `DwellTime` parameter below for actual dwell time). It is required for unwarping distortions using field maps. Note that beyond just in-plane acceleration, a variety of other manipulations to the phase encoding need to be accounted for properly, including partial fourier, phase oversampling, phase resolution, phase field-of-view and interpolation.<sup>2</sup> This parameter is REQUIRED if corresponding fieldmap data is present.                                                                                                                  |
 | TotalReadoutTime               | RECOMMENDED           | [number][]    | This is actually the "effective" total readout time , defined as the readout duration, specified in seconds, that would have generated data with the given level of distortion. It is NOT the actual, physical duration of the readout train. If `EffectiveEchoSpacing` has been properly computed, it is just `EffectiveEchoSpacing * (ReconMatrixPE - 1)`.<sup>3</sup> . This parameter is REQUIRED if corresponding "field/distortion" maps acquired with opposing phase encoding directions are present (see 8.9.4).                                                                                                                                                                                                                                                                                                  |
+| MixingTime                     | RECOMMENDED           | [number][]    | In the context of a stimulated- and spin-echo 3D EPI sequence for B1+ mapping, corresponds to the interval between spin- and stimulated-echo pulses. In the context of a diffusion-weighted double spin-echo sequence, corresponds to the interval between two successive diffusion sensitizing gradients.                                                                                                                                                                                                                                                                                            |
 
 <sup>2</sup>Conveniently, for Siemens data, this value is easily obtained as
 `1 / (BWPPPE * ReconMatrixPE)`, where BWPPPE is the

From 43f5bbf77680e48a0bed1db2e7a09ee08244ef79 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Tue, 8 Dec 2020 01:33:06 -0500
Subject: [PATCH 23/83] Consistency

---
 src/99-appendices/11-qmri.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index d73ede06bb..42897b5942 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -413,9 +413,9 @@ and the parallel imaging acceleration factor in PE direction.
 
 ### Radiofrequency (RF) field mapping
 
-General note:
+General notes:
 
-Some RF file collections call for the use of special notations that cannot be resolved by
+* Some RF file collections call for the use of special notations that cannot be resolved by
 by entities that can generalize to other applications. Instead of introducing an entity
 that is exclusive to a single application, method developers who commonly use these file
 collections for the `MPM` application reached the consensus on the use of `acq` entity to

From 3de00fb972fbd0951cc96d6c603114c15bdf8d58 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Tue, 8 Dec 2020 20:01:56 -0500
Subject: [PATCH 24/83] Address comment

---
 .../01-magnetic-resonance-imaging-data.md                    | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 444d64199b..2dad2fe91e 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -276,9 +276,8 @@ them, visit the [qMRI appendix](../99-appendices/11-qmri.md).
 ### Deprecated suffixes
 
 Some suffixes that were available in versions of the specification prior to
-1.5.0. have been deprecated. These suffixes generate inconsistencies and/or 
-ambiguities with additional suffixes added in version 1.5.0. Therefore, they
-are not recommended for use in new datasets.
+1.5.0. have been deprecated. These suffixes are ambiguous and have been superseded
+by more precise conventions. Therefore, they are not recommended for use in new datasets.
 They are, however, still valid suffixes, to maintain backwards compatibility.
 
 The following suffixes are valid, but SHOULD NOT be used for new BIDS compatible

From c6924f500286de786692069896ee53ab8660daa8 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Tue, 8 Dec 2020 20:46:36 -0500
Subject: [PATCH 25/83] map units

---
 .../01-magnetic-resonance-imaging-data.md                 | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 2dad2fe91e..27434e91cc 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -250,16 +250,16 @@ constitute parametric maps. Currently supported parametric maps include:
 | True transverse relaxation rate map          | R2map     | In seconds<sup>-1</sup> (1/s). R2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                            |
 | Observed transverse relaxation rate map      | R2starmap | In seconds<sup>-1</sup> (1/s). R2-star maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                       |
 | Proton density map                           | PDmap     | In arbitrary units (arbitrary). PD maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                           |
-| Magnetization transfer ratio map             | MTRmap    | In percentage (%). MTR maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                                       |
+| Magnetization transfer ratio map             | MTRmap    | In arbitrary units (arbitrary). MTR maps are REQUIRED to use this suffix regardless of the method used to generate them. MTRmap intensity values are RECOMMENDED to be represented in percentage in the range of 0-100%.                                                                                                                                                                                                                                                                                                                                                                                                       |
 | Magnetization transfer saturation map        | MTsat     | In arbitrary units (arbitrary). MTsat maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                        |
 | Homogeneous (flat) T1-weighted MP2RAGE image | UNIT1     | In arbitrary units (arbitrary). UNIT1 images are REQUIRED to use this suffix regardless of the method used to generate them. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from from `T1w`.                                                                                                                                                        |
 | T1 in rotating frame (T1 rho) map            | T1rho     | In seconds (s). T1-rho maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                                       |
-| Myelin water fraction map                    | MWFmap    | In percentage (%). MWF maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                                       |
+| Myelin water fraction map                    | MWFmap    | In arbitrary units (arbitrary). MWF maps are REQUIRED to use this suffix regardless of the method used to generate them. MWF intensity values are RECOMMENDED to be represented in percentage in the range of 0-100%.                                                                                                                                                                                                                                                                                                                                                                                                       |
 | Macromolecular tissue volume (MTV) map       | MTVmap    | In arbitrary units (arbitrary). MTV maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                          |
 | Combined PD/T2 map                           | PDT2map   | In arbitrary units (arbitrary). Combined PD/T2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                               |
 | Quantitative susceptibility map (QSM)        | Chimap    | In parts per million (ppm). QSM allows for determining the underlying magnetic susceptibility of tissue (Chi) ([Wang & Liu, 2014](https://onlinelibrary.wiley.com/doi/10.1002/mrm.25358)). Chi maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                               |
-| RF transmit field map                        | TB1map    | In percent units (p.u.). Radio frequency (RF) transmit field maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                 |
-| RF receive sensitivity map                   | RB1map    | In percent units (p.u.). Radio frequency (RF) receive sensitivity maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                            |
+| RF transmit field map                        | TB1map    | In arbitrary units (arbitrary). Radio frequency (RF) transmit (B1+) field maps are REQUIRED to use this suffix regardless of the method used to generate them. TB1map intensity values are RECOMMENDED to be represented as percent multiplicative factors such that FlipAngle<sub>effective</sub> = B1+<sub>intensity</sub>*FlipAngle<sub>nominal</sub> .                                                                                                                                                                                                                                                                                                                                                                    |
+| RF receive sensitivity map                   | RB1map    | In arbitrary units (arbitrary). Radio frequency (RF) receive (B1-) sensitivity maps are REQUIRED to use this suffix regardless of the method used to generate them. RB1map intensity values are RECOMMENDED to be represented as percent multiplicative factors such that Amplitude<sub>effective</sub> = B1-<sub>intensity</sub>*Amplitude<sub>ideal</sub>.                                                                                                                                                                                                                                                                                                                                                            |
 | Observed signal amplitude (S0) map           | S0map     | In arbitrary units (arbitrary). For a multi-echo (typically fMRI) sequence, S0 maps index the baseline signal before exponential (T2-star) signal decay. In other words: the exponential of the intercept for a linear decay model across log-transformed echos. For more information, please see, for example, [the tedana documentation](https://tedana.readthedocs.io/en/latest/approach.html#monoexponential-decay-model-fit). S0 maps are RECOMMENDED to use this suffix if derived from an ME-FMRI dataset. |
 | Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (arbitrary). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications (e.g. variable flip angle T1 mapping.                                                                                                                                                                                                                                          |
 

From ed54b4cd258cbbbf38ddb777cb25b740abaf6f4e Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Mon, 14 Dec 2020 14:39:24 +0100
Subject: [PATCH 26/83] Super minot textual edits

---
 src/99-appendices/11-qmri.md | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 42897b5942..7bd0084e3a 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -308,7 +308,7 @@ define the flavor of the application (fourth column) along with the conditional
 required metadata field (second column).
 
 A derived qMRI application becomes avaiable if all the optional metadata fields
-listed for the respective file collection suffix is provided for the data. In addition,
+listed for the respective file collection suffix are provided for the data. In addition,
 conditional rules based on the value of a given required metada field can be set
 for the description of a derived qMRI application. Note that the value of this
 required metadata is fixed across constituent images of a file collection and defined
@@ -469,9 +469,10 @@ entity MUST index the images as follows:
 #### `TB1AFI` specific notes
 
 This method calculates a B1<sup>+</sup> map from two images acquired at two
-interleaved excitation repetition times (TR). Note that there is not an entity 
-for the TR and its definition depends on the modality (`functional` or `anatomical`)
-in the specification. 
+interleaved excitation repetition times (TR). Note that there is no entity 
+for the TR that can be used to label the files corresponding to the two
+repetition times and the definition of repetition time depends on the modality
+(`functional` or `anatomical`) in the specification. 
 
 Therefore, to properly identify constituents of this particular method, values of 
 the `acq` entity SHOULD begin with either `tr1` (lower TR) or `tr2` (higher TR) 
@@ -543,4 +544,4 @@ entries:
          ├── sub-01_acq-body_RB1COR.json
          ├── sub-01_acq-head_RB1COR.nii.gz (Head coil)
          └── sub-01_acq-head_RB1COR.json
-```
\ No newline at end of file
+```

From 60aae1a70e39ff90210c7037025b651237deca9e Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Mon, 14 Dec 2020 14:49:44 +0100
Subject: [PATCH 27/83] Some small textual fixes in 10-file-collections

---
 src/99-appendices/10-file-collections.md | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/src/99-appendices/10-file-collections.md b/src/99-appendices/10-file-collections.md
index 986dfc399e..4266dcb65c 100644
--- a/src/99-appendices/10-file-collections.md
+++ b/src/99-appendices/10-file-collections.md
@@ -1,10 +1,8 @@
 # Appendix X: File collections
 
-To give context to the use of [entity-linked file collections](../02-common-principles.md#file-name-structure),
-applications concerned with this common principle are listed by descriptive tables
-under their respective modalities.
+Here, some concrete use-cases of [entity-linked file collections](../02-common-principles.md#file-name-structure) are listed using descriptive tables, organized by modality.
 
-Note that the tables in this appendix catalog applications where the use of
+The tables in this appendix catalog applications where the use of
 a file collection is REQUIRED.
 
 Certain entitites interlink the files in a file collection through a metadata field.
@@ -56,7 +54,7 @@ sub-<label>/[ses-<label>/]
 | TB1DAM  | flip                                                         | Double-angle B1+ mapping           | The double-angle B1<sup>+</sup> method ([Insko and Bolinger 1993](https://www.sciencedirect.com/science/article/abs/pii/S1064185883711332)) is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation flip angles. Common sequence types for this application include spin echo and echo planar imaging.                                                                                                |
 | TB1EPI  | flip, echo                                                   | B1<sup>+</sup> mapping with 3D EPI | This B1<sup>+</sup> mapping method ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)) is based on two EPI readouts to acquire spin echo (SE) and stimulated echo (STE) images at multiple flip angles in one sequence, used in the calculation of deviations from the nominal flip angle.                                                                                                                                                                             |
 | TB1AFI  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Actual Flip Angle Imaging (AFI)    | This method ([Yarnykh 2007](https://dx.doi.org/10.1002/mrm.21120)) calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence                                                                                                                                                                                                                                                                      |
-| TB1TFL  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `tfl_b1_map`               | B1<sup>+</sup> data acquired using `tfl_b1_map` product sequence by Siemens based on the method by [Chung et al. (2010)](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.22423). The sequence generates one ~anatomical image and one scaled flip angle map.                                                                                                                                                                                                                |
+| TB1TFL  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `tfl_b1_map`               | B1<sup>+</sup> data acquired using `tfl_b1_map` product sequence by Siemens based on the method by [Chung et al. (2010)](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.22423). The sequence generates one anatomical image and one scaled flip angle map.                                                                                                                                                                                                                 |
 | TB1RMF  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `rf_map`                   | B1<sup>+</sup> data acquired using `rf_map` product sequence by Siemens                                                                                                                                                                                                                                                                                                                                                                                                          |
 | TB1SRGE | `flip`, `inv`                                                | SA2RAGE                            | Saturation-prepared with 2 rapid gradient echoes (SA2RAGE) uses a ratio of two saturation recovery images with different time delays, and a simulated look-up table to estimate B1+ ([Eggenschwiler et al. 2011](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.23145)). This sequence can also be used in conjunction with MP2RAGE T1 mapping to iteratively improve B1+ and T1 map estimation ([Marques & Gruetter 2013](https://doi.org/10.1371/journal.pone.0069294)). |
 | RB1COR  | Please see the [qMRI appendix](../99-appendices/11-qmri.md)  | B1<sup>-</sup> field correction    | Low resolution images acquired by the body coil (in the gantry of the scanner) and the head coil using identical acquisition parameters to generate a combined sensitivity map as described in [Papp et al. (2016)](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.26058)                                                                                                                                                                                                  |

From f23d59f521efec0240e4fd66eac7adb5f4097d7d Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 21 Dec 2020 10:47:06 +0100
Subject: [PATCH 28/83] re-render entity table after rebase

using  python tools/bids_schema.py entities src/schema/ src/99-appendices/04-entity-table.md
---
 src/99-appendices/04-entity-table.md | 348 +++++++++++++++++++++++----
 1 file changed, 302 insertions(+), 46 deletions(-)

diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index b7d5dd3c65..2bbd081438 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -2,53 +2,309 @@
   This file is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
   Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#updating-the-schema
 -->
-# Appendix IV: Entity table
+# Appendix IX: Entities
 
 This section compiles the entities (key-value pairs) described throughout this
-specification, and establishes a common order within a filename. 
-For example, if a file has an acquisition and reconstruction label, the
-acquisition entity must precede the reconstruction entity.
-REQUIRED and OPTIONAL entities for a given file type are denoted.
-Entity formats indicate whether the value is alphanumeric
-(`<label>`) or numeric (`<index>`).
+specification, and describes each.
 
 A general introduction to entities is given in the section on
-[file name structure](../02-common-principles.md#file-name-structure),
-while entity definitions are in [Appendix IX](09-entities.md).
-
-## Magnetic Resonance Imaging
-
-| Entity                                                                                         | Subject                             | Session                             | Task                                  | Acquisition                         | Contrast Enhancing Agent          | Reconstruction                      | Phase-Encoding Direction            | Run                                 | Corresponding Modality              | Echo                                  | Part                                  | Recording                                       |
-|------------------------------------------------------------------------------------------------|-------------------------------------|-------------------------------------|---------------------------------------|-------------------------------------|-----------------------------------|-------------------------------------|-------------------------------------|-------------------------------------|-------------------------------------|---------------------------------------|---------------------------------------|-------------------------------------------------|
-| Format                                                                                         | [`sub-<label>`](09-entities.md#sub) | [`ses-<label>`](09-entities.md#ses) | [`task-<label>`](09-entities.md#task) | [`acq-<label>`](09-entities.md#acq) | [`ce-<label>`](09-entities.md#ce) | [`rec-<label>`](09-entities.md#rec) | [`dir-<label>`](09-entities.md#dir) | [`run-<index>`](09-entities.md#run) | [`mod-<label>`](09-entities.md#mod) | [`echo-<index>`](09-entities.md#echo) | [`part-<label>`](09-entities.md#part) | [`recording-<label>`](09-entities.md#recording) |
-| anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            |                                     |                                       | OPTIONAL                              |                                                 |
-| anat<br>(defacemask)                                                                           | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            | OPTIONAL                            |                                       |                                       |                                                 |
-| dwi<br>(dwi sbref)                                                                             | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                   |                                     | OPTIONAL                            | OPTIONAL                            |                                     |                                       | OPTIONAL                              |                                                 |
-| fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap)                     | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                   |                                     |                                     | OPTIONAL                            |                                     |                                       |                                       |                                                 |
-| fmap<br>(epi)                                                                                  | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          |                                     | REQUIRED                            | OPTIONAL                            |                                     |                                       |                                       |                                                 |
-| func<br>(bold cbv sbref)                                                                       | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            | OPTIONAL                            | OPTIONAL                            |                                     | OPTIONAL                              | OPTIONAL                              |                                                 |
-| func<br>(phase events)                                                                         | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            | OPTIONAL                            | OPTIONAL                            |                                     | OPTIONAL                              |                                       |                                                 |
-| func<br>(physio stim)                                                                          | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            |                                   | OPTIONAL                            |                                     | OPTIONAL                            |                                     |                                       |                                       | OPTIONAL                                        |
-
-## Encephalography (EEG, iEEG, and MEG)
-
-| Entity                     | Subject                             | Session                             | Task                                  | Acquisition                         | Run                                 | Processed (on device)                 | Space                                   | Split                                   |
-|----------------------------|-------------------------------------|-------------------------------------|---------------------------------------|-------------------------------------|-------------------------------------|---------------------------------------|-----------------------------------------|-----------------------------------------|
-| Format                     | [`sub-<label>`](09-entities.md#sub) | [`ses-<label>`](09-entities.md#ses) | [`task-<label>`](09-entities.md#task) | [`acq-<label>`](09-entities.md#acq) | [`run-<index>`](09-entities.md#run) | [`proc-<label>`](09-entities.md#proc) | [`space-<label>`](09-entities.md#space) | [`split-<index>`](09-entities.md#split) |
-| eeg<br>(eeg)               | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            |                                       |                                         |                                         |
-| ieeg<br>(ieeg)             | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            |                                       |                                         |                                         |
-| meg<br>(meg)               | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            | OPTIONAL                              |                                         | OPTIONAL                                |
-| meg<br>(headshape)         | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                     |                                       | OPTIONAL                                |                                         |
-| meg<br>(markers)           | REQUIRED                            | OPTIONAL                            | OPTIONAL                              | OPTIONAL                            |                                     |                                       | OPTIONAL                                |                                         |
-| channels<br>(meg eeg ieeg) | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            |                                       |                                         |                                         |
-| electrodes<br>(eeg ieeg)   | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                     |                                       | OPTIONAL                                |                                         |
-| events<br>(meg eeg ieeg)   | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            |                                       |                                         |                                         |
-| photo<br>(meg eeg ieeg)    | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                     |                                       |                                         |                                         |
-
-## Behavioral Data
-
-| Entity               | Subject                             | Session                             | Task                                  | Acquisition                         | Run                                 | Recording                                       |
-|----------------------|-------------------------------------|-------------------------------------|---------------------------------------|-------------------------------------|-------------------------------------|-------------------------------------------------|
-| Format               | [`sub-<label>`](09-entities.md#sub) | [`ses-<label>`](09-entities.md#ses) | [`task-<label>`](09-entities.md#task) | [`acq-<label>`](09-entities.md#acq) | [`run-<index>`](09-entities.md#run) | [`recording-<label>`](09-entities.md#recording) |
-| beh<br>(stim physio) | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            | OPTIONAL                                        |
-| beh<br>(events beh)  | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            |                                                 |
+[file name structure](../02-common-principles.md#file-name-structure).
+
+The ordering of entities and whether it is allowed, OPTIONAL, or REQUIRED for
+each is given in the [Entity Table](04-entity-table.md).
+
+## sub
+
+Full name: Subject
+
+Format: `sub-<label>`
+
+Definition: A person or animal participating in the study.
+
+## ses
+
+Full name: Session
+
+Format: `ses-<label>`
+
+Definition: A logical grouping of neuroimaging and behavioral data consistent across
+subjects.
+Session can (but doesn't have to) be synonymous to a visit in a
+longitudinal study.
+In general, subjects will stay in the scanner during one session.
+However, for example, if a subject has to leave the scanner room and then
+be re-positioned on the scanner bed, the set of MRI acquisitions will still
+be considered as a session and match sessions acquired in other subjects.
+Similarly, in situations where different data types are obtained over
+several visits (for example fMRI on one day followed by DWI the day after)
+those can be grouped in one session.
+Defining multiple sessions is appropriate when several identical or similar
+data acquisitions are planned and performed on all -or most- subjects,
+often in the case of some intervention between sessions
+(for example, training).
+
+## task
+
+Full name: Task
+
+Format: `task-<label>`
+
+Definition: Each task has a unique label that MUST only consist of letters and/or
+numbers (other characters, including spaces and underscores, are not
+allowed).
+Those labels MUST be consistent across subjects and sessions.
+
+## acq
+
+Full name: Acquisition
+
+Format: `acq-<label>`
+
+Definition: The `acq-<label>` key/value pair corresponds to a custom label the
+user MAY use to distinguish a different set of parameters used for
+acquiring the same modality.
+For example this should be used when a study includes two T1w images - one
+full brain low resolution and and one restricted field of view but high
+resolution.
+In such case two files could have the following names:
+`sub-01_acq-highres_T1w.nii.gz` and `sub-01_acq-lowres_T1w.nii.gz`, however
+the user is free to choose any other label than highres and lowres as long
+as they are consistent across subjects and sessions.
+In case different sequences are used to record the same modality
+(for example, RARE and FLASH for T1w)
+this field can also be used to make that distinction.
+At what level of detail to make the distinction (for example,
+just between RARE and FLASH, or between RARE, FLASH, and FLASHsubsampled)
+remains at the discretion of the researcher.
+
+## ce
+
+Full name: Contrast Enhancing Agent
+
+Format: `ce-<label>`
+
+Definition: The `ce-<label>` key/value can be used to distinguish
+sequences using different contrast enhanced images.
+The label is the name of the contrast agent.
+The key `ContrastBolusIngredient` MAY be also be added in the JSON file,
+with the same label.
+
+## rec
+
+Full name: Reconstruction
+
+Format: `rec-<label>`
+
+Definition: The `rec-<label>` key/value can be used to distinguish
+different reconstruction algorithms (for example ones using motion
+correction).
+
+## dir
+
+Full name: Phase-Encoding Direction
+
+Format: `dir-<label>`
+
+Definition: The `dir-<label>` key/value can be set to an arbitrary alphanumeric label
+(for example, `dir-LR` or `dir-AP`) to distinguish different phase-encoding
+directions.
+
+## run
+
+Full name: Run
+
+Format: `run-<index>`
+
+Definition: If several scans of the same modality are acquired they MUST be indexed
+with a key-value pair: `_run-1`, `_run-2`, ..., `_run-<index>`
+(only nonnegative integers are allowed for the `<index>`).
+When there is only one scan of a given type the run key MAY be omitted.
+
+## mod
+
+Full name: Corresponding Modality
+
+Format: `mod-<label>`
+
+Definition: The `mod-<label>` key/value pair corresponds to modality label for defacing
+masks, for example, T1w, inplaneT1, referenced by a defacemask image.
+For example, `sub-01_mod-T1w_defacemask.nii.gz`.
+
+## echo
+
+Full name: Echo
+
+Format: `echo-<index>`
+
+Definition: If files belonging to an entity-linked file collection are acquired at different
+echo times, the `_echo-<index>` key/value pair MUST be used to distinguish
+individual files.
+This entity represents the `EchoTime` metadata field. Please note that the `<index>`
+denotes the number/index (in the form of a nonnegative integer), not the
+`EchoTime` value which needs to be stored in the field `EchoTime` of the separate
+JSON file.
+
+## flip
+
+Full name: Flip Angle
+
+Format: `flip-<index>`
+
+Definition: If files belonging to an entity-linked file collection are acquired at different
+flip angles, the `_flip-<index>` key/value pair MUST be used to distinguish
+individual files.
+This entity represents the `FlipAngle` metadata field. Please note that the `<index>`
+denotes the number/index (in the form of a nonnegative integer), not the `FlipAngle`
+value which needs to be stored in the field `FlipAngle` of the separate JSON file.
+
+## inv
+
+Full name: Inversion Time
+
+Format: `inv-<index>`
+
+Definition: If files belonging to an entity-linked file collection are acquired at different
+inversion times, the `_inv-<index>` key/value pair MUST be used to distinguish
+individual files.
+This entity represents the `InversionTime` metadata field. Please note that the `<index>`
+denotes the number/index (in the form of a nonnegative integer), not the `InversionTime`
+value which needs to be stored in the field `InversionTime` of the separate JSON file.
+
+## mt
+
+Full name: Magnetization Transfer
+
+Format: `mt-<label>`
+
+Definition: If files belonging to an entity-linked file collection are acquired at different
+magnetization transfer (MT) states, the `_mt-<label>` key/value pair MUST be used to
+distinguish individual files.
+This entity represents the `MTState` metadata field. Allowed label values for this
+entity are `on` and `off`, for images acquired in presence and absence of an MT pulse,
+respectively.
+
+## part
+
+Full name: Part
+
+Format: `part-<label>`
+
+Definition: This entity is used to indicate which component of the complex
+representation of the MRI signal is represented in voxel data.
+The `part-<label>` key/value pair is associated with the DICOM tag
+`0008,9208`.
+Allowed label values for this entity are `phase`, `mag`, `real` and `imag`,
+which are typically used in `part-mag`/`part-phase` or
+`part-real`/`part-imag` pairs of files.
+
+Phase images MAY be in radians or in arbitrary units.
+The sidecar JSON file MUST include the units of the `phase` image.
+The possible options are `rad` or `arbitrary`.
+
+When there is only a magnitude image of a given type, the `part` key MAY be
+omitted.
+
+## recording
+
+Full name: Recording
+
+Format: `recording-<label>`
+
+Definition: More than one continuous recording file can be included (with different
+sampling frequencies).
+In such case use different labels.
+For example: `_recording-contrast`, `_recording-saturation`.
+
+## proc
+
+Full name: Processed (on device)
+
+Format: `proc-<label>`
+
+Definition: The proc label is analogous to rec for MR and denotes a variant of a file
+that was a result of particular processing performed on the device.
+This is useful for files produced in particular by Elekta’s MaxFilter
+(for example, sss, tsss, trans, quat or mc),
+which some installations impose to be run on raw data because of active
+shielding software corrections before the MEG data can actually be
+exploited.
+
+## space
+
+Full name: Space
+
+Format: `space-<label>`
+
+Definition: The space entity can be used to indicate
+the way in which electrode positions are interpreted
+(for EEG/MEG/iEEG data) or
+the spatial reference to which a file has been aligned (for MRI data).
+The space label needs to be taken from the list in Appendix VIII.
+
+For EEG/MEG/iEEG data, this entity can be applied to raw data, but
+for other data types, it is restricted to derivative data.
+
+## split
+
+Full name: Split
+
+Format: `split-<index>`
+
+Definition: In the case of long data recordings that exceed a file size of 2Gb, the
+.fif files are conventionally split into multiple parts.
+Each of these files has an internal pointer to the next file.
+This is important when renaming these split recordings to the BIDS
+convention.
+
+Instead of a simple renaming, files should be read in and saved under their
+new names with dedicated tools like MNE, which will ensure that not only
+the file names, but also the internal file pointers will be updated.
+It is RECOMMENDED that .fif files with multiple parts use the
+`split-<index>` entity to indicate each part.
+
+## res
+
+Full name: Resolution
+
+Format: `res-<label>`
+
+Definition: Resolution of regularly sampled N-dimensional data.
+MUST have a corresponding `Resolution` metadata field to provide
+interpretation.
+
+This entity is only applicable to derivative data.
+
+## den
+
+Full name: Density
+
+Format: `den-<label>`
+
+Definition: Density of non-parametric surfaces.
+MUST have a corresponding `Density` metadata field to provide
+interpretation.
+
+This entity is only applicable to derivative data.
+
+## label
+
+Full name: Label
+
+Format: `label-<label>`
+
+Definition: Tissue-type label, following a prescribed vocabulary.
+Applies to binary masks and probabilistic/partial volume segmentations
+that describe a single tissue type.
+
+This entity is only applicable to derivative data.
+
+## desc
+
+Full name: Description
+
+Format: `desc-<label>`
+
+Definition: When necessary to distinguish two files that do not otherwise have a
+distinguishing entity, the `_desc-<label>` keyword-value SHOULD be used.
+
+This entity is only applicable to derivative data.

From 553ca4a9b12bfd3e2756bd8140170efd89b3388e Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 21 Dec 2020 10:51:28 +0100
Subject: [PATCH 29/83] fix call to use entitytable, not entities

---
 src/99-appendices/04-entity-table.md | 357 +++++----------------------
 1 file changed, 55 insertions(+), 302 deletions(-)

diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 2bbd081438..da16d20ebc 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -2,309 +2,62 @@
   This file is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
   Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#updating-the-schema
 -->
-# Appendix IX: Entities
+# Appendix IV: Entity table
 
 This section compiles the entities (key-value pairs) described throughout this
-specification, and describes each.
+specification, and establishes a common order within a filename. 
+For example, if a file has an acquisition and reconstruction label, the
+acquisition entity must precede the reconstruction entity.
+REQUIRED and OPTIONAL entities for a given file type are denoted.
+Entity formats indicate whether the value is alphanumeric
+(`<label>`) or numeric (`<index>`).
 
 A general introduction to entities is given in the section on
-[file name structure](../02-common-principles.md#file-name-structure).
-
-The ordering of entities and whether it is allowed, OPTIONAL, or REQUIRED for
-each is given in the [Entity Table](04-entity-table.md).
-
-## sub
-
-Full name: Subject
-
-Format: `sub-<label>`
-
-Definition: A person or animal participating in the study.
-
-## ses
-
-Full name: Session
-
-Format: `ses-<label>`
-
-Definition: A logical grouping of neuroimaging and behavioral data consistent across
-subjects.
-Session can (but doesn't have to) be synonymous to a visit in a
-longitudinal study.
-In general, subjects will stay in the scanner during one session.
-However, for example, if a subject has to leave the scanner room and then
-be re-positioned on the scanner bed, the set of MRI acquisitions will still
-be considered as a session and match sessions acquired in other subjects.
-Similarly, in situations where different data types are obtained over
-several visits (for example fMRI on one day followed by DWI the day after)
-those can be grouped in one session.
-Defining multiple sessions is appropriate when several identical or similar
-data acquisitions are planned and performed on all -or most- subjects,
-often in the case of some intervention between sessions
-(for example, training).
-
-## task
-
-Full name: Task
-
-Format: `task-<label>`
-
-Definition: Each task has a unique label that MUST only consist of letters and/or
-numbers (other characters, including spaces and underscores, are not
-allowed).
-Those labels MUST be consistent across subjects and sessions.
-
-## acq
-
-Full name: Acquisition
-
-Format: `acq-<label>`
-
-Definition: The `acq-<label>` key/value pair corresponds to a custom label the
-user MAY use to distinguish a different set of parameters used for
-acquiring the same modality.
-For example this should be used when a study includes two T1w images - one
-full brain low resolution and and one restricted field of view but high
-resolution.
-In such case two files could have the following names:
-`sub-01_acq-highres_T1w.nii.gz` and `sub-01_acq-lowres_T1w.nii.gz`, however
-the user is free to choose any other label than highres and lowres as long
-as they are consistent across subjects and sessions.
-In case different sequences are used to record the same modality
-(for example, RARE and FLASH for T1w)
-this field can also be used to make that distinction.
-At what level of detail to make the distinction (for example,
-just between RARE and FLASH, or between RARE, FLASH, and FLASHsubsampled)
-remains at the discretion of the researcher.
-
-## ce
-
-Full name: Contrast Enhancing Agent
-
-Format: `ce-<label>`
-
-Definition: The `ce-<label>` key/value can be used to distinguish
-sequences using different contrast enhanced images.
-The label is the name of the contrast agent.
-The key `ContrastBolusIngredient` MAY be also be added in the JSON file,
-with the same label.
-
-## rec
-
-Full name: Reconstruction
-
-Format: `rec-<label>`
-
-Definition: The `rec-<label>` key/value can be used to distinguish
-different reconstruction algorithms (for example ones using motion
-correction).
-
-## dir
-
-Full name: Phase-Encoding Direction
-
-Format: `dir-<label>`
-
-Definition: The `dir-<label>` key/value can be set to an arbitrary alphanumeric label
-(for example, `dir-LR` or `dir-AP`) to distinguish different phase-encoding
-directions.
-
-## run
-
-Full name: Run
-
-Format: `run-<index>`
-
-Definition: If several scans of the same modality are acquired they MUST be indexed
-with a key-value pair: `_run-1`, `_run-2`, ..., `_run-<index>`
-(only nonnegative integers are allowed for the `<index>`).
-When there is only one scan of a given type the run key MAY be omitted.
-
-## mod
-
-Full name: Corresponding Modality
-
-Format: `mod-<label>`
-
-Definition: The `mod-<label>` key/value pair corresponds to modality label for defacing
-masks, for example, T1w, inplaneT1, referenced by a defacemask image.
-For example, `sub-01_mod-T1w_defacemask.nii.gz`.
-
-## echo
-
-Full name: Echo
-
-Format: `echo-<index>`
-
-Definition: If files belonging to an entity-linked file collection are acquired at different
-echo times, the `_echo-<index>` key/value pair MUST be used to distinguish
-individual files.
-This entity represents the `EchoTime` metadata field. Please note that the `<index>`
-denotes the number/index (in the form of a nonnegative integer), not the
-`EchoTime` value which needs to be stored in the field `EchoTime` of the separate
-JSON file.
-
-## flip
-
-Full name: Flip Angle
-
-Format: `flip-<index>`
-
-Definition: If files belonging to an entity-linked file collection are acquired at different
-flip angles, the `_flip-<index>` key/value pair MUST be used to distinguish
-individual files.
-This entity represents the `FlipAngle` metadata field. Please note that the `<index>`
-denotes the number/index (in the form of a nonnegative integer), not the `FlipAngle`
-value which needs to be stored in the field `FlipAngle` of the separate JSON file.
-
-## inv
-
-Full name: Inversion Time
-
-Format: `inv-<index>`
-
-Definition: If files belonging to an entity-linked file collection are acquired at different
-inversion times, the `_inv-<index>` key/value pair MUST be used to distinguish
-individual files.
-This entity represents the `InversionTime` metadata field. Please note that the `<index>`
-denotes the number/index (in the form of a nonnegative integer), not the `InversionTime`
-value which needs to be stored in the field `InversionTime` of the separate JSON file.
-
-## mt
-
-Full name: Magnetization Transfer
-
-Format: `mt-<label>`
-
-Definition: If files belonging to an entity-linked file collection are acquired at different
-magnetization transfer (MT) states, the `_mt-<label>` key/value pair MUST be used to
-distinguish individual files.
-This entity represents the `MTState` metadata field. Allowed label values for this
-entity are `on` and `off`, for images acquired in presence and absence of an MT pulse,
-respectively.
-
-## part
-
-Full name: Part
-
-Format: `part-<label>`
-
-Definition: This entity is used to indicate which component of the complex
-representation of the MRI signal is represented in voxel data.
-The `part-<label>` key/value pair is associated with the DICOM tag
-`0008,9208`.
-Allowed label values for this entity are `phase`, `mag`, `real` and `imag`,
-which are typically used in `part-mag`/`part-phase` or
-`part-real`/`part-imag` pairs of files.
-
-Phase images MAY be in radians or in arbitrary units.
-The sidecar JSON file MUST include the units of the `phase` image.
-The possible options are `rad` or `arbitrary`.
-
-When there is only a magnitude image of a given type, the `part` key MAY be
-omitted.
-
-## recording
-
-Full name: Recording
-
-Format: `recording-<label>`
-
-Definition: More than one continuous recording file can be included (with different
-sampling frequencies).
-In such case use different labels.
-For example: `_recording-contrast`, `_recording-saturation`.
-
-## proc
-
-Full name: Processed (on device)
-
-Format: `proc-<label>`
-
-Definition: The proc label is analogous to rec for MR and denotes a variant of a file
-that was a result of particular processing performed on the device.
-This is useful for files produced in particular by Elekta’s MaxFilter
-(for example, sss, tsss, trans, quat or mc),
-which some installations impose to be run on raw data because of active
-shielding software corrections before the MEG data can actually be
-exploited.
-
-## space
-
-Full name: Space
-
-Format: `space-<label>`
-
-Definition: The space entity can be used to indicate
-the way in which electrode positions are interpreted
-(for EEG/MEG/iEEG data) or
-the spatial reference to which a file has been aligned (for MRI data).
-The space label needs to be taken from the list in Appendix VIII.
-
-For EEG/MEG/iEEG data, this entity can be applied to raw data, but
-for other data types, it is restricted to derivative data.
-
-## split
-
-Full name: Split
-
-Format: `split-<index>`
-
-Definition: In the case of long data recordings that exceed a file size of 2Gb, the
-.fif files are conventionally split into multiple parts.
-Each of these files has an internal pointer to the next file.
-This is important when renaming these split recordings to the BIDS
-convention.
-
-Instead of a simple renaming, files should be read in and saved under their
-new names with dedicated tools like MNE, which will ensure that not only
-the file names, but also the internal file pointers will be updated.
-It is RECOMMENDED that .fif files with multiple parts use the
-`split-<index>` entity to indicate each part.
-
-## res
-
-Full name: Resolution
-
-Format: `res-<label>`
-
-Definition: Resolution of regularly sampled N-dimensional data.
-MUST have a corresponding `Resolution` metadata field to provide
-interpretation.
-
-This entity is only applicable to derivative data.
-
-## den
-
-Full name: Density
-
-Format: `den-<label>`
-
-Definition: Density of non-parametric surfaces.
-MUST have a corresponding `Density` metadata field to provide
-interpretation.
-
-This entity is only applicable to derivative data.
-
-## label
-
-Full name: Label
-
-Format: `label-<label>`
-
-Definition: Tissue-type label, following a prescribed vocabulary.
-Applies to binary masks and probabilistic/partial volume segmentations
-that describe a single tissue type.
-
-This entity is only applicable to derivative data.
-
-## desc
-
-Full name: Description
-
-Format: `desc-<label>`
-
-Definition: When necessary to distinguish two files that do not otherwise have a
-distinguishing entity, the `_desc-<label>` keyword-value SHOULD be used.
-
-This entity is only applicable to derivative data.
+[file name structure](../02-common-principles.md#file-name-structure),
+while entity definitions are in [Appendix IX](09-entities.md).
+
+## Magnetic Resonance Imaging
+
+| Entity                                                                                                                                      | Subject                             | Session                             | Task                                  | Acquisition                         | Contrast Enhancing Agent          | Reconstruction                      | Phase-Encoding Direction            | Run                                 | Corresponding Modality              | Echo                                  | Flip Angle                            | Inversion Time                      | Magnetization Transfer            | Part                                  | Recording                                       |
+|---------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------|-------------------------------------|---------------------------------------|-------------------------------------|-----------------------------------|-------------------------------------|-------------------------------------|-------------------------------------|-------------------------------------|---------------------------------------|---------------------------------------|-------------------------------------|-----------------------------------|---------------------------------------|-------------------------------------------------|
+| Format                                                                                                                                      | [`sub-<label>`](09-entities.md#sub) | [`ses-<label>`](09-entities.md#ses) | [`task-<label>`](09-entities.md#task) | [`acq-<label>`](09-entities.md#acq) | [`ce-<label>`](09-entities.md#ce) | [`rec-<label>`](09-entities.md#rec) | [`dir-<label>`](09-entities.md#dir) | [`run-<index>`](09-entities.md#run) | [`mod-<label>`](09-entities.md#mod) | [`echo-<index>`](09-entities.md#echo) | [`flip-<index>`](09-entities.md#flip) | [`inv-<index>`](09-entities.md#inv) | [`mt-<label>`](09-entities.md#mt) | [`part-<label>`](09-entities.md#part) | [`recording-<label>`](09-entities.md#recording) |
+| anat<br>(T1w T2w PDw T2starw FLAIR inplaneT1 inplaneT2 PDT2 angio)                                                                          | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            |                                     |                                       |                                       |                                     |                                   | OPTIONAL                              |                                                 |
+| anat<br>(T1map T2map T2starmap R1map R2map R2starmap PDmap MTRmap MTsat UNIT1 T1rho MWFmap MTVmap PDT2map Chimap TB1map RB1map S0map M0map) | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            |                                     |                                       |                                       |                                     |                                   |                                       |                                                 |
+| anat<br>(defacemask)                                                                                                                        | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            | OPTIONAL                            |                                       |                                       |                                     |                                   |                                       |                                                 |
+| anat<br>(MESE MEGRE)                                                                                                                        | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            |                                     | REQUIRED                              |                                       |                                     |                                   | OPTIONAL                              |                                                 |
+| anat<br>(VFA)                                                                                                                               | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            |                                     |                                       | REQUIRED                              |                                     |                                   | OPTIONAL                              |                                                 |
+| anat<br>(IRT1)                                                                                                                              | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            |                                     |                                       |                                       | REQUIRED                            |                                   | OPTIONAL                              |                                                 |
+| anat<br>(MP2RAGE)                                                                                                                           | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            |                                     | OPTIONAL                              | REQUIRED                              | REQUIRED                            |                                   | OPTIONAL                              |                                                 |
+| anat<br>(MPM MTS)                                                                                                                           | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            |                                     | OPTIONAL                              | REQUIRED                              |                                     | REQUIRED                          | OPTIONAL                              |                                                 |
+| anat<br>(MTR)                                                                                                                               | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            |                                     |                                       |                                       |                                     | REQUIRED                          | OPTIONAL                              |                                                 |
+| dwi<br>(dwi sbref)                                                                                                                          | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                   |                                     | OPTIONAL                            | OPTIONAL                            |                                     |                                       |                                       |                                     |                                   | OPTIONAL                              |                                                 |
+| fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap)                                                                  | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                   |                                     |                                     | OPTIONAL                            |                                     |                                       |                                       |                                     |                                   |                                       |                                                 |
+| fmap<br>(epi)                                                                                                                               | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          |                                     | REQUIRED                            | OPTIONAL                            |                                     |                                       |                                       |                                     |                                   |                                       |                                                 |
+| fmap<br>(TB1DAM)                                                                                                                            | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            |                                     |                                       | REQUIRED                              |                                     |                                   | OPTIONAL                              |                                                 |
+| fmap<br>(TB1EPI)                                                                                                                            | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            |                                     | REQUIRED                              | REQUIRED                              |                                     |                                   | OPTIONAL                              |                                                 |
+| func<br>(bold cbv sbref)                                                                                                                    | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            | OPTIONAL                            | OPTIONAL                            |                                     | OPTIONAL                              |                                       |                                     |                                   | OPTIONAL                              |                                                 |
+| func<br>(phase events)                                                                                                                      | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            | OPTIONAL                            | OPTIONAL                            |                                     | OPTIONAL                              |                                       |                                     |                                   |                                       |                                                 |
+| func<br>(physio stim)                                                                                                                       | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            |                                   | OPTIONAL                            |                                     | OPTIONAL                            |                                     |                                       |                                       |                                     |                                   |                                       | OPTIONAL                                        |
+
+## Encephalography (EEG, iEEG, and MEG)
+
+| Entity                     | Subject                             | Session                             | Task                                  | Acquisition                         | Run                                 | Processed (on device)                 | Space                                   | Split                                   |
+|----------------------------|-------------------------------------|-------------------------------------|---------------------------------------|-------------------------------------|-------------------------------------|---------------------------------------|-----------------------------------------|-----------------------------------------|
+| Format                     | [`sub-<label>`](09-entities.md#sub) | [`ses-<label>`](09-entities.md#ses) | [`task-<label>`](09-entities.md#task) | [`acq-<label>`](09-entities.md#acq) | [`run-<index>`](09-entities.md#run) | [`proc-<label>`](09-entities.md#proc) | [`space-<label>`](09-entities.md#space) | [`split-<index>`](09-entities.md#split) |
+| eeg<br>(eeg)               | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            |                                       |                                         |                                         |
+| ieeg<br>(ieeg)             | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            |                                       |                                         |                                         |
+| meg<br>(meg)               | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            | OPTIONAL                              |                                         | OPTIONAL                                |
+| meg<br>(headshape)         | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                     |                                       | OPTIONAL                                |                                         |
+| meg<br>(markers)           | REQUIRED                            | OPTIONAL                            | OPTIONAL                              | OPTIONAL                            |                                     |                                       | OPTIONAL                                |                                         |
+| channels<br>(meg eeg ieeg) | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            |                                       |                                         |                                         |
+| electrodes<br>(eeg ieeg)   | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                     |                                       | OPTIONAL                                |                                         |
+| events<br>(meg eeg ieeg)   | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            |                                       |                                         |                                         |
+| photo<br>(meg eeg ieeg)    | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                     |                                       |                                         |                                         |
+
+## Behavioral Data
+
+| Entity               | Subject                             | Session                             | Task                                  | Acquisition                         | Run                                 | Recording                                       |
+|----------------------|-------------------------------------|-------------------------------------|---------------------------------------|-------------------------------------|-------------------------------------|-------------------------------------------------|
+| Format               | [`sub-<label>`](09-entities.md#sub) | [`ses-<label>`](09-entities.md#ses) | [`task-<label>`](09-entities.md#task) | [`acq-<label>`](09-entities.md#acq) | [`run-<index>`](09-entities.md#run) | [`recording-<label>`](09-entities.md#recording) |
+| beh<br>(stim physio) | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            | OPTIONAL                                        |
+| beh<br>(events beh)  | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                            |                                                 |

From cacefee052a841747181c92512477a43c77b3151 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 21 Dec 2020 10:52:42 +0100
Subject: [PATCH 30/83] fix 09-entities using correct schema call

---
 src/99-appendices/09-entities.md | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/src/99-appendices/09-entities.md b/src/99-appendices/09-entities.md
index 38ee57d17b..2bbd081438 100644
--- a/src/99-appendices/09-entities.md
+++ b/src/99-appendices/09-entities.md
@@ -2,15 +2,10 @@
   This file is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
   Follow https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md#updating-the-schema
 -->
-# Appendix IV: Entity table
+# Appendix IX: Entities
 
 This section compiles the entities (key-value pairs) described throughout this
-specification, and establishes a common order within a filename. 
-For example, if a file has an acquisition and reconstruction label, the
-acquisition entity must precede the reconstruction entity.
-REQUIRED and OPTIONAL entities for a given file type are denoted.
-Entity formats indicate whether the value is alphanumeric
-(`<label>`) or numeric (`<index>`).
+specification, and describes each.
 
 A general introduction to entities is given in the section on
 [file name structure](../02-common-principles.md#file-name-structure).

From 94584e95d107b033e2c619924741f97c2c36b04a Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 30 Dec 2020 14:51:32 -0500
Subject: [PATCH 31/83] Drop latin phrases

---
 src/99-appendices/11-qmri.md | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 7bd0084e3a..e76dc2d312 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -2,10 +2,10 @@
 
 Quantitative MRI (qMRI) is a collection of methods aiming at generating parametric
 maps that can characterize underlying tissue properties. Unlike that of conventional
-MR images (e.g., `T1w`, `T2w`), intensity values of quantitative maps are not represented
+MR images (for example, `T1w`, `T2w`), intensity values of quantitative maps are not represented
 in an arbitrary grayscale range. Instead, these maps are represented either in absolute 
-physical units (e.g., `seconds` for `T1map`), or within an application dependent range of
-arbitrary units (e.g., myelin water fraction `MWFmap` in brain).
+physical units (for example, `seconds` for `T1map`), or within an application dependent range of
+arbitrary units (for example, myelin water fraction `MWFmap` in brain).
 
 ## Organization of qMRI data in BIDS
 
@@ -32,7 +32,7 @@ The common concept of [entity-linked file collections](../02-common-principles.m
 application by creating logical groups of input files through `suffix` and certain entities
 representing acquisition parameters (`echo`, `flip`,`inv`, `mt`) or file parts (`part`).
 
-If a qMRI file collection is intended for creating structural quantitative maps (e.g., `T1map`),
+If a qMRI file collection is intended for creating structural quantitative maps (for example, `T1map`),
 files belonging to that collection are stored in the `anat` subfolder. Below is an example 
 file collection for `MP2RAGE`: 
 
@@ -137,7 +137,7 @@ Explanation of the table:
 * The metadata fields listed in the REQUIRED column are needed to perform a minimum viable
 qMRI processing for the corresponding `file collection`.
 * Note that some of the metadata fields may be constant across different files in a file
-collection, yet still required as an input (e.g. `NumberShots` in `MP2AGE`). Such metadata
+collection, yet still required as an input (for example, `NumberShots` in `MP2AGE`). Such metadata
 fields MUST be provided in the accompanying json files.
 * The metadata fields listed in the OPTIONAL column can be used to form different flavors
 of an existing file collection suffix, despensing with the need for introducing a new
@@ -227,7 +227,7 @@ is RECOMMENDED to include additional metadata fields listed in the following tab
 | ------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- |
 | `BasedOn`                       | List of files in a file collection to generate the map. Fieldmaps are also listed, if involved in the processing.            |
 | `EstimationReference`           | Reference to the study/studies on which the implementation is based.                                                         |
-| `EstimationAlgorithm`           | Type of algoritm used to perform fitting (e.g. linear, non-linear, LM etc.)                                                  |
+| `EstimationAlgorithm`           | Type of algoritm used to perform fitting (for example, linear, non-linear, LM etc.)                                                  |
 | `Units`                         | Units of the maps, in accordance with the BIDS specification.                                                                |
 
 Example:
@@ -276,10 +276,10 @@ sub-01_T1map.json
 ## Deriving the intended qMRI application from an ambiguous file collection
 
 Certain file colleciton suffixes may refer to a generic data collection regime such 
-as variable flip angle (VFA), rather than a more specific acquisition, e.g.,
+as variable flip angle (VFA), rather than a more specific acquisition, for example,
 magnetization prepared two gradient echoes (MP2RAGE). Such generic acquisitions
 can serve as a basis to derive various qMRI applications by changes to the acquisition
-sequence (e.g. readout) type or by varying additional scan parameters.
+sequence (for example, readout) type or by varying additional scan parameters.
 
 If such an inheritance relationship is applicable between an already existing file
 collection and a new qMRI application to be included in the specification, the inheritor
@@ -334,7 +334,7 @@ introduce a new suffix:
 
 * All qMRI-relevant file collection suffixes are capitalized.
 * Unless the pulse sequence is exclusively associated with a specific qMRI application
-(e.g. `MP2RAGE`), sequence names are not used as suffixes.
+(for example, `MP2RAGE`), sequence names are not used as suffixes.
 * File collection suffixes for qMRI applications attain a clear description
 of the qMRI method that they relate to in the [file collections appendix]((../99-appendices/10-file-collections.md#magnetic-resonance-imaging)).
 Hyperlinks to example applications and reference method articles are encouraged
@@ -406,7 +406,7 @@ Further information about other `MP2RAGE` qMRI protocol fields can be found [her
 
 Calculation of `before` and `after` entries for `NumberShots` metadata field of `TB1SRGE`
 is more involved than that of `MP2RAGE`. The formula can be found [here](https://github.com/JosePMarques/MP2RAGE-related-scripts/blob/a405df30ac2c617d29d8b1b16025aaa911e86370/DemoForR1Correction.m#L17), which requires 
-information about `BaseResolution` (i.e. image matrix size in PE direction), partial Fourier
+information about `BaseResolution` (that is, image matrix size in PE direction), partial Fourier
 fraction in the PE direction, number of reference lines for parallel imaging acceleration
 and the parallel imaging acceleration factor in PE direction.
 
@@ -437,7 +437,7 @@ At each `FlipAngle`, the `TB1EPI` suffix lists two images acquired at two echo t
 The first echo is a spin echo (SE) formed by the pulses alpha-2alpha. However, the 
 second echo in this method is generated in a different fashion compared to a typical
 MESE acquisition. The second echo is a stimulated echo (STE) that is formed by an 
-additional alpha pulse (i.e., alpha-2alpha-alpha).
+additional alpha pulse (that is, alpha-2alpha-alpha).
 
 The `FlipAngle` value corresponds to the nominal flip angle value of the STE pulse.
 The nominal FA value of the SE pulse is twice this value.

From d16bd402834819f489317bb104383f76daac8358 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 30 Dec 2020 22:05:44 -0500
Subject: [PATCH 32/83] Fix double quotes

---
 src/99-appendices/11-qmri.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index e76dc2d312..4746f3e146 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -254,12 +254,12 @@ sub-01_T1map.json
 
 <<Parameters that are constant across files in the (parent) file collection>>
 
-“MagneticFieldStrength”: “3”,
-“Manufacturer”: “Siemens”,
-“ManufacturerModelName”: “TrioTim”,
-“InstitutionName”: “xxx”,
-“PulseSequenceType”: “SPGR”,
-“PulseSequenceDetails”: “Information beyond the sequence type that identifies
+"MagneticFieldStrength”: "3”,
+"Manufacturer”: "Siemens”,
+"ManufacturerModelName”: "TrioTim”,
+"InstitutionName”: "xxx”,
+"PulseSequenceType”: "SPGR”,
+"PulseSequenceDetails”: "Information beyond the sequence type that identifies
  specific pulse sequence used (VB version, if not standard, Siemens WIP XXX
  ersion ### sequence written by xx using a version compiled on mm/dd/yyyy/)”,
 "RepetitionTimeExcitation": "35",

From 274e1f82eade7d6d74d59bb6b5d9ebcf0b4c34a4 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 30 Dec 2020 22:31:42 -0500
Subject: [PATCH 33/83] Codeblock type fix

---
 src/99-appendices/11-qmri.md | 31 ++++++++++++++++---------------
 1 file changed, 16 insertions(+), 15 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 4746f3e146..94ad3c1dae 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -36,7 +36,7 @@ If a qMRI file collection is intended for creating structural quantitative maps
 files belonging to that collection are stored in the `anat` subfolder. Below is an example 
 file collection for `MP2RAGE`: 
 
-```
+```text
 └── sub-01/
      └── anat/
          ├── sub-01_inv-1_part-mag_MP2RAGE.nii.gz
@@ -52,7 +52,7 @@ maps. As these images do not convey substantial structural information, respecti
 of RF fieldmaps are stored in the `fmap` subfolder. Below is an example file collection for RF transmit
 field map `TB1EPI`:
 
-```
+```text
 └── sub-01/
      └── fmap/
          ├── sub-01_fa-1_echo-1_TB1EPI.nii.gz
@@ -73,7 +73,7 @@ Regardless of how they are obtained (pre- or post-generated), qMRI maps are stor
 `derivatives` folder. For example a `T1map` can be generated from an `MP2RAGE` file collection
 using either options. If the map is post-generated:
 
-```
+```text
  ds-example/
  └── derivatives/
      └── qMRI-software-name/
@@ -87,7 +87,7 @@ using either options. If the map is post-generated:
 
 If the map is pre-generated, for example, by a Siemens scanner:
 
-```
+```text
  ds-example/
  └── derivatives/
      └── Siemens/
@@ -165,7 +165,7 @@ As qMRI maps are stored as derivatives, they are subjected to the metadata requi
 
 An example `dataset_description.json` for a qMRI map derivatives folder: 
 
-```
+```text
  ds-example/
  └── derivatives/
      └── qMRLab/
@@ -178,9 +178,9 @@ An example `dataset_description.json` for a qMRI map derivatives folder:
                  └── sub-01_M0map.json
 ```
 
+dataset_description.json:
 
-```
-dataset_description.json: 
+```text
 {
   "Name": "qMRLab Outputs",
   "BIDSVersion": "1.5.0",
@@ -232,13 +232,14 @@ is RECOMMENDED to include additional metadata fields listed in the following tab
 
 Example:
 
-```Text
+```text
 sub-01_T1map.nii.gz
 sub-01_T1map.json
 ```
 
-```
-sub-01_T1map.json
+sub-01_T1map.json:
+
+```text
 {
 
 <<Parameter injected by the software/pipeline>>
@@ -389,7 +390,7 @@ Formula:
 If NumberShots is an array of numbers such that `"NumberShots": [before, after]`, the values of
 `before` and `after` are calculated as follows ([reference](https://github.com/JosePMarques/MP2RAGE-related-scripts/blob/a405df30ac2c617d29d8b1b16025aaa911e86370/func/bids_T1B1correct.m#L16)):
 
-```
+```text
 before = SlicesPerSlab*(SlicePartialFourier - 0.5)
 after  = SlicesPerSlab/2
 ```
@@ -453,7 +454,7 @@ files:
 To properly identify constituents of this particular method, values of the `echo`
 entity MUST index the images as follows:  
 
-```
+```text
 └── sub-01/
      └── fmap/
          ├── sub-01_echo-1_flip-1_TB1EPI.nii.gz (SE)
@@ -484,7 +485,7 @@ and MAY be followed by freeform entries:
 |`_acq-tr1Test`|`_acq-tr2Test`|Acquisition `Test`|
 |`_acq-tr1Retest`|`_acq-tr2Retest`|Acquisition `Retest`|
 
-```
+```text
 └── sub-01/
      └── fmap/
          ├── sub-01_acq-tr1_TB1AFI.nii.gz
@@ -509,7 +510,7 @@ by freeform entries:
 |`_acq-anatTest`|`_acq-fampTest`|Acquisition `Test`|
 |`_acq-anatRetest`|`_acq-fampRetest`|Acquisition `Retest`|
 
-```
+```text
 └── sub-01/
      └── fmap/
          ├── sub-01_acq-anat_TB1TFL.nii.gz 
@@ -537,7 +538,7 @@ entries:
 |`_acq-bodyPDw`|`_acq-headPDw`|`PDw` for `MPM`|
 |`_acq-bodyT1w`|`_acq-headT1w`|`T1w` for `MPM`|
 
-```
+```text
 └── sub-01/
      └── fmap/
          ├── sub-01_acq-body_RB1COR.nii.gz (Body coil)

From 0bda72f8ada0eac968406f82018633a7957f700a Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 30 Dec 2020 22:37:34 -0500
Subject: [PATCH 34/83] Fix article hyperlinks --> DOI

---
 src/99-appendices/10-file-collections.md | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/99-appendices/10-file-collections.md b/src/99-appendices/10-file-collections.md
index 4266dcb65c..56af28e1c1 100644
--- a/src/99-appendices/10-file-collections.md
+++ b/src/99-appendices/10-file-collections.md
@@ -32,14 +32,14 @@ sub-<label>/[ses-<label>/]
 
 | Suffix  | Linking entities      | Application                                | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
 |---------|-----------------------|--------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| VFA     | flip                  | Variable flip angle                        | The VFA method involves at least two spoiled gradient echo (SPGR) of steady-state free precession (SSFP) images acquired at different flip angles. Depending on the provided metadata fields and the sequence type, data may be eligible for DESPOT1, DESPOT2 and their variants ([Deoni et al. 2005](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.20314)).                                                                                           |
-| IRT1    | inv, part             | Inversion recovery T1 mapping              | The IRT1 method involves multiple inversion recovery spin-echo images acquired at different inversion times ([Barral et al. 2010](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.22497)).                                                                                                                                                                                                                                                               |
-| MP2RAGE | flip, inv, echo, part | Magnetization prepared two gradient echoes | The MP2RAGE method is a special protocol that collects several images at different flip angles and inversion times to create a parametric T1map by combining the magnitude and phase images ([Marques et al. 2010](https://www.sciencedirect.com/science/article/pii/S1053811909010738?casa_token=u_CYBx4hi7IAAAAA:3w0cMTyU5jA1BdFs0s5oVcQeqF2tZho0iJ9d4N1kExfaX27v9-JnWacF6mbEp_lMKZ64CvoTl8k)).                                                               |
+| VFA     | flip                  | Variable flip angle                        | The VFA method involves at least two spoiled gradient echo (SPGR) of steady-state free precession (SSFP) images acquired at different flip angles. Depending on the provided metadata fields and the sequence type, data may be eligible for DESPOT1, DESPOT2 and their variants ([Deoni et al. 2005](https://doi.org/10.1002/mrm.20314)).                                                                                           |
+| IRT1    | inv, part             | Inversion recovery T1 mapping              | The IRT1 method involves multiple inversion recovery spin-echo images acquired at different inversion times ([Barral et al. 2010](https://doi.org/10.1002/mrm.22497)).                                                                                                                                                                                                                                                               |
+| MP2RAGE | flip, inv, echo, part | Magnetization prepared two gradient echoes | The MP2RAGE method is a special protocol that collects several images at different flip angles and inversion times to create a parametric T1map by combining the magnitude and phase images ([Marques et al. 2010](https://doi.org/10.1016/j.neuroimage.2009.10.002)).                                                               |
 | MESE    | echo                  | Multi-echo spin-echo                       | The MESE method involves multiple spin echo images acquired at different echo times and is primarily used for T2 mapping. Please note that this suffix is not intended for the logical grouping of images acquired using an Echo Planar Imaging (EPI) readout.                                                                                                                                                                                                |
 | MEGRE   | echo                  | Multi-echo gradient-echo                   | Anatomical gradient echo images acquired at different echo times. Please note that this suffix is not intended for the logical grouping of images acquired using an Echo Planar Imaging (EPI) readout.                                                                                                                                                                                                                                                        |
 | MTR     | mt                    | Magnetization transfer ratio               | This method is to calculate a semi-quantitative magnetization transfer ratio map.                                                                                                                                                                                                                                                                                                                                                                             |
-| MTS     | flip, mt              | Magnetization transfer saturation          | This method is to calculate a semi-quantitative magnetization transfer saturation index map. The MTS method involves three sets of anatomical images that differ in terms of application of a magnetization transfer RF pulse (MTon or MToff) and flip angle ([Helms et al. 2008](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.21732)).                                                                                                               |
-| MPM     | flip, mt, echo, part  | Multi-parametric mapping                   | The MPM approaches (a.k.a hMRI) involves the acquisition of highly-similar anatomical images that differ in terms of application of a magnetization transfer RF pulse (MTon or MToff), flip angle and (optionally) echo time and magnitue/phase parts ([Weiskopf et al. 2013](https://www.frontiersin.org/articles/10.3389/fnins.2013.00095/full)). See [here](https://owncloud.gwdg.de/index.php/s/iv2TOQwGy4FGDDZ) for suggested MPM acquisition protocols. |
+| MTS     | flip, mt              | Magnetization transfer saturation          | This method is to calculate a semi-quantitative magnetization transfer saturation index map. The MTS method involves three sets of anatomical images that differ in terms of application of a magnetization transfer RF pulse (MTon or MToff) and flip angle ([Helms et al. 2008](https://doi.org/10.1002/mrm.21732)).                                                                                                               |
+| MPM     | flip, mt, echo, part  | Multi-parametric mapping                   | The MPM approaches (a.k.a hMRI) involves the acquisition of highly-similar anatomical images that differ in terms of application of a magnetization transfer RF pulse (MTon or MToff), flip angle and (optionally) echo time and magnitue/phase parts ([Weiskopf et al. 2013](https://doi.org/10.3389/fnins.2013.00095)). See [here](https://owncloud.gwdg.de/index.php/s/iv2TOQwGy4FGDDZ) for suggested MPM acquisition protocols. |
 
 ### Fieldmap data
 
@@ -51,10 +51,10 @@ sub-<label>/[ses-<label>/]
 
 | Suffix  | Meta-data relevant entity                                    | Application                        | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
 |---------|--------------------------------------------------------------|------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| TB1DAM  | flip                                                         | Double-angle B1+ mapping           | The double-angle B1<sup>+</sup> method ([Insko and Bolinger 1993](https://www.sciencedirect.com/science/article/abs/pii/S1064185883711332)) is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation flip angles. Common sequence types for this application include spin echo and echo planar imaging.                                                                                                |
-| TB1EPI  | flip, echo                                                   | B1<sup>+</sup> mapping with 3D EPI | This B1<sup>+</sup> mapping method ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)) is based on two EPI readouts to acquire spin echo (SE) and stimulated echo (STE) images at multiple flip angles in one sequence, used in the calculation of deviations from the nominal flip angle.                                                                                                                                                                             |
-| TB1AFI  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Actual Flip Angle Imaging (AFI)    | This method ([Yarnykh 2007](https://dx.doi.org/10.1002/mrm.21120)) calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence                                                                                                                                                                                                                                                                      |
-| TB1TFL  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `tfl_b1_map`               | B1<sup>+</sup> data acquired using `tfl_b1_map` product sequence by Siemens based on the method by [Chung et al. (2010)](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.22423). The sequence generates one anatomical image and one scaled flip angle map.                                                                                                                                                                                                                 |
+| TB1DAM  | flip                                                         | Double-angle B1+ mapping           | The double-angle B1<sup>+</sup> method ([Insko and Bolinger 1993](https://doi.org/10.1006/jmra.1993.1133)) is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation flip angles. Common sequence types for this application include spin echo and echo planar imaging.                                                                                                |
+| TB1EPI  | flip, echo                                                   | B1<sup>+</sup> mapping with 3D EPI | This B1<sup>+</sup> mapping method ([Jiru and Klose 2006](https://doi.org/10.1002/mrm.21083)) is based on two EPI readouts to acquire spin echo (SE) and stimulated echo (STE) images at multiple flip angles in one sequence, used in the calculation of deviations from the nominal flip angle.                                                                                                                                                                             |
+| TB1AFI  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Actual Flip Angle Imaging (AFI)    | This method ([Yarnykh 2007](https://doi.org/10.1002/mrm.21120)) calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence                                                                                                                                                                                                                                                                      |
+| TB1TFL  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `tfl_b1_map`               | B1<sup>+</sup> data acquired using `tfl_b1_map` product sequence by Siemens based on the method by [Chung et al. (2010)](https://doi.org/10.1002/mrm.22423). The sequence generates one anatomical image and one scaled flip angle map.                                                                                                                                                                                                                 |
 | TB1RMF  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `rf_map`                   | B1<sup>+</sup> data acquired using `rf_map` product sequence by Siemens                                                                                                                                                                                                                                                                                                                                                                                                          |
-| TB1SRGE | `flip`, `inv`                                                | SA2RAGE                            | Saturation-prepared with 2 rapid gradient echoes (SA2RAGE) uses a ratio of two saturation recovery images with different time delays, and a simulated look-up table to estimate B1+ ([Eggenschwiler et al. 2011](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.23145)). This sequence can also be used in conjunction with MP2RAGE T1 mapping to iteratively improve B1+ and T1 map estimation ([Marques & Gruetter 2013](https://doi.org/10.1371/journal.pone.0069294)). |
-| RB1COR  | Please see the [qMRI appendix](../99-appendices/11-qmri.md)  | B1<sup>-</sup> field correction    | Low resolution images acquired by the body coil (in the gantry of the scanner) and the head coil using identical acquisition parameters to generate a combined sensitivity map as described in [Papp et al. (2016)](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.26058)                                                                                                                                                                                                  |
+| TB1SRGE | `flip`, `inv`                                                | SA2RAGE                            | Saturation-prepared with 2 rapid gradient echoes (SA2RAGE) uses a ratio of two saturation recovery images with different time delays, and a simulated look-up table to estimate B1+ ([Eggenschwiler et al. 2011](https://doi.org/10.1002/mrm.23145)). This sequence can also be used in conjunction with MP2RAGE T1 mapping to iteratively improve B1+ and T1 map estimation ([Marques & Gruetter 2013](https://doi.org/10.1371/journal.pone.0069294)). |
+| RB1COR  | Please see the [qMRI appendix](../99-appendices/11-qmri.md)  | B1<sup>-</sup> field correction    | Low resolution images acquired by the body coil (in the gantry of the scanner) and the head coil using identical acquisition parameters to generate a combined sensitivity map as described in [Papp et al. (2016)](https://doi.org/10.1002/mrm.26058)                                                                                                                                                                                                  |

From 8e22a7f80c83ee7d52751efe4c4d6c832bbdce0b Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 30 Dec 2020 22:47:46 -0500
Subject: [PATCH 35/83] Punctuation fixes

---
 src/99-appendices/10-file-collections.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/99-appendices/10-file-collections.md b/src/99-appendices/10-file-collections.md
index 56af28e1c1..37645aca9e 100644
--- a/src/99-appendices/10-file-collections.md
+++ b/src/99-appendices/10-file-collections.md
@@ -53,8 +53,8 @@ sub-<label>/[ses-<label>/]
 |---------|--------------------------------------------------------------|------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
 | TB1DAM  | flip                                                         | Double-angle B1+ mapping           | The double-angle B1<sup>+</sup> method ([Insko and Bolinger 1993](https://doi.org/10.1006/jmra.1993.1133)) is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation flip angles. Common sequence types for this application include spin echo and echo planar imaging.                                                                                                |
 | TB1EPI  | flip, echo                                                   | B1<sup>+</sup> mapping with 3D EPI | This B1<sup>+</sup> mapping method ([Jiru and Klose 2006](https://doi.org/10.1002/mrm.21083)) is based on two EPI readouts to acquire spin echo (SE) and stimulated echo (STE) images at multiple flip angles in one sequence, used in the calculation of deviations from the nominal flip angle.                                                                                                                                                                             |
-| TB1AFI  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Actual Flip Angle Imaging (AFI)    | This method ([Yarnykh 2007](https://doi.org/10.1002/mrm.21120)) calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence                                                                                                                                                                                                                                                                      |
+| TB1AFI  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Actual Flip Angle Imaging (AFI)    | This method ([Yarnykh 2007](https://doi.org/10.1002/mrm.21120)) calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence.                                                                                                                                                                                                                                                                      |
 | TB1TFL  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `tfl_b1_map`               | B1<sup>+</sup> data acquired using `tfl_b1_map` product sequence by Siemens based on the method by [Chung et al. (2010)](https://doi.org/10.1002/mrm.22423). The sequence generates one anatomical image and one scaled flip angle map.                                                                                                                                                                                                                 |
-| TB1RMF  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `rf_map`                   | B1<sup>+</sup> data acquired using `rf_map` product sequence by Siemens                                                                                                                                                                                                                                                                                                                                                                                                          |
+| TB1RMF  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `rf_map`                   | B1<sup>+</sup> data acquired using `rf_map` product sequence by Siemens.                                                                                                                                                                                                                                                                                                                                                                                                          |
 | TB1SRGE | `flip`, `inv`                                                | SA2RAGE                            | Saturation-prepared with 2 rapid gradient echoes (SA2RAGE) uses a ratio of two saturation recovery images with different time delays, and a simulated look-up table to estimate B1+ ([Eggenschwiler et al. 2011](https://doi.org/10.1002/mrm.23145)). This sequence can also be used in conjunction with MP2RAGE T1 mapping to iteratively improve B1+ and T1 map estimation ([Marques & Gruetter 2013](https://doi.org/10.1371/journal.pone.0069294)). |
-| RB1COR  | Please see the [qMRI appendix](../99-appendices/11-qmri.md)  | B1<sup>-</sup> field correction    | Low resolution images acquired by the body coil (in the gantry of the scanner) and the head coil using identical acquisition parameters to generate a combined sensitivity map as described in [Papp et al. (2016)](https://doi.org/10.1002/mrm.26058)                                                                                                                                                                                                  |
+| RB1COR  | Please see the [qMRI appendix](../99-appendices/11-qmri.md).  | B1<sup>-</sup> field correction    | Low resolution images acquired by the body coil (in the gantry of the scanner) and the head coil using identical acquisition parameters to generate a combined sensitivity map as described in [Papp et al. (2016)](https://doi.org/10.1002/mrm.26058).                                                                                                                                                                                                  |

From 0630127aa5b55211a64bad4a63cca0c127ad8c67 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 30 Dec 2020 23:02:27 -0500
Subject: [PATCH 36/83] Add section links iof italics

---
 src/99-appendices/11-qmri.md | 20 +++++++++-----------
 1 file changed, 9 insertions(+), 11 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 94ad3c1dae..978ec36bc5 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -141,8 +141,8 @@ collection, yet still required as an input (for example, `NumberShots` in `MP2AG
 fields MUST be provided in the accompanying json files.
 * The metadata fields listed in the OPTIONAL column can be used to form different flavors
 of an existing file collection suffix, despensing with the need for introducing a new
-suffix. See _Deriving the intended qMRI application from an ambiguos file collection_
-section for details.
+suffix. See [deriving the intended qMRI application from an ambiguos file collection](#Deriving-the-intended-qMRI-application-from-an-ambiguous-file-collection) section
+for details.
 
 #### Field maps
 
@@ -313,7 +313,7 @@ listed for the respective file collection suffix are provided for the data. In a
 conditional rules based on the value of a given required metada field can be set
 for the description of a derived qMRI application. Note that the value of this
 required metadata is fixed across constituent images of a file collection and defined
-in the _Method-specific priority levels for qMRI file collections_ section above.
+in [this section](#Method-specific-priority-levels-for-qMRI-file-collections).
 
 For example, if the optional metadata field of `PulseSequenceType` is SPGR
 for a collection of anatomical images listed by the `VFA` suffix, the data
@@ -322,10 +322,9 @@ metadata field has the value of `SSFP`, and the `SpoilingRFPhaseIncrement` is
 provided as a metadata field, then the dataset becomes eligible for `DESPOT2`
 T2 fitting application.
 
-Please note that optional metadata fields listed in the _Deriving the intended qMRI_
-_application from an ambiguous file collection_ table are included in the optional (third)
-column of the _Method-specific priority levels for qMRI file collections_ table for
-the consistency of this appendix.
+Please note that optional metadata fields listed in the [deriving the intended qMRI
+application from an ambiguous file collection table](#Deriving-the-intended-qMRI-application-from-an-ambiguous-file-collection) are included in the optional (third)
+column of [the priority levels table](#Method-specific-priority-levels-for-qMRI-file-collections) for the consistency of this appendix.
 
 ## Introducing a new qMRI file collection
 
@@ -338,13 +337,12 @@ introduce a new suffix:
 (for example, `MP2RAGE`), sequence names are not used as suffixes.
 * File collection suffixes for qMRI applications attain a clear description
 of the qMRI method that they relate to in the [file collections appendix]((../99-appendices/10-file-collections.md#magnetic-resonance-imaging)).
-Hyperlinks to example applications and reference method articles are encouraged
+* Hyperlinks to example applications and reference method articles are encouraged
 whenever possible.
 * If it is possible to derive a qMRI application from an already existing file collection
 suffix by defining a set of logical conditions over the metadata fields, the tables of
-_Deriving the intended qMRI application from an ambiguous file collection_ and the
-_Method-specific priority levels for qMRI file collections/Anatomy_ sections are extended 
-instead of introducing a new suffix.
+[deriving the intended qMRI application from an ambiguous file collection](#Deriving-the-intended-qMRI-application-from-an-ambiguous-file-collection) and the
+[anatomy data priority levels](#Anatomy-imaging-data) sections are extended instead of introducing a new suffix.
 
 ## Application-specific notes for qMRI file collections
 

From ace0ae870c2e818c2b5f6d2813176c3bc44ee785 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 30 Dec 2020 23:05:43 -0500
Subject: [PATCH 37/83] Drop etc.

---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 978ec36bc5..08e22ab239 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -227,7 +227,7 @@ is RECOMMENDED to include additional metadata fields listed in the following tab
 | ------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- |
 | `BasedOn`                       | List of files in a file collection to generate the map. Fieldmaps are also listed, if involved in the processing.            |
 | `EstimationReference`           | Reference to the study/studies on which the implementation is based.                                                         |
-| `EstimationAlgorithm`           | Type of algoritm used to perform fitting (for example, linear, non-linear, LM etc.)                                                  |
+| `EstimationAlgorithm`           | Type of algoritm used to perform fitting (for example, linear, non-linear, LM and such)                                      |
 | `Units`                         | Units of the maps, in accordance with the BIDS specification.                                                                |
 
 Example:

From b97f0a21fd67b01e3bdad289f2b1e3fa96973e38 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 30 Dec 2020 23:08:15 -0500
Subject: [PATCH 38/83] Rm Latin phrase

---
 .../01-magnetic-resonance-imaging-data.md                   | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 27434e91cc..2972a73106 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -148,11 +148,11 @@ non-parametric structural MR images include:
 
 | **Name**                                   | `suffix`         | **Description**                                                                                                                                   |
 | ------------------------------------------ | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- |
-| T1 weighted images                         | T1w              | In arbitrary units (abitrary). The contrast of these images is mainly determined by spatial variations in the longitudinal relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively short repetition and echo times. To achieve this weigthing in gradient-echo images, again, short repetition and echo times are selected; however, at relatively large flip angles. Another common approach to increase T1 weighting in gradient-echo images is to add an inversion preparation block to the beginning of the imaging sequence (e.g. `TurboFLASH` or `MP-RAGE`).                           |
+| T1 weighted images                         | T1w              | In arbitrary units (abitrary). The contrast of these images is mainly determined by spatial variations in the longitudinal relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively short repetition and echo times. To achieve this weigthing in gradient-echo images, again, short repetition and echo times are selected; however, at relatively large flip angles. Another common approach to increase T1 weighting in gradient-echo images is to add an inversion preparation block to the beginning of the imaging sequence (for example, `TurboFLASH` or `MP-RAGE`).                           |
 | T2 weighted images                         | T2w              | In arbitrary units (abitrary). The contrast of these images is mainly determined by spatial variations in the (true) transverse relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively long repetition and echo times. Generally, gradient echo sequences are not the most suitable option for achieving T2 weighting, as their contrast natively depends on T2-star rather than on T2.        |
 | Proton density (PD) weighted images        | PDw              | In arbitrary units (abitrary). The contrast of these images is mainly determined by spatial variations in the spin density (1H) of the imaged specimen. In spin-echo sequences this contrast is achieved at short repetition and long echo times. In a gradient-echo acquisition, PD weighting dominates the contrast at long repetition and short echo times, and at small flip angles.|
 | T2star weighted images                     | T2starw          | In arbitrary units (abitrary). The contrast of these images is mainly determined by spatial variations in the (observed) transverse relaxation time of the imaged specimen. In spin-echo sequences, this effect is negated as the excitation is followed by an inversion pulse. The contrast of gradient-echo images natively depends on T2-star effects. However, for T2-star variation to dominate the image contrast, gradient-echo acquisitions are carried out at long repetition and echo times, and at small flip angles.                                                                                                     |
-| Fluid attenuated inversion recovery images | FLAIR            | In arbitrary units (abitrary). Structural images with predominant T2 contribution (a.k.a T2-FLAIR), in which signal from fluids (e.g., CSF) is nulled out by adjusting inversion time, coupled with notably long repetition and echo times.                                                  |
+| Fluid attenuated inversion recovery images | FLAIR            | In arbitrary units (abitrary). Structural images with predominant T2 contribution (a.k.a T2-FLAIR), in which signal from fluids (for example, CSF) is nulled out by adjusting inversion time, coupled with notably long repetition and echo times.                                                  |
 | Inplane T1                                 | inplaneT1        | In arbitrary units (abitrary). T1 weighted structural image matched to a functional (task) image.                                                                                  |
 | Inplane T2                                 | inplaneT2        | In arbitrary units (abitrary). T2 weighted structural image matched to a functional (task) image.                                                                                  |
 | PD and T2 weighted images                  | PDT2             | In arbitrary units (abitrary). PDw and T2w images acquired using a dual echo FSE sequence through view sharing process ([Johnson et al. 1994](https://pubmed.ncbi.nlm.nih.gov/8010268/)).                                      |
@@ -261,7 +261,7 @@ constitute parametric maps. Currently supported parametric maps include:
 | RF transmit field map                        | TB1map    | In arbitrary units (arbitrary). Radio frequency (RF) transmit (B1+) field maps are REQUIRED to use this suffix regardless of the method used to generate them. TB1map intensity values are RECOMMENDED to be represented as percent multiplicative factors such that FlipAngle<sub>effective</sub> = B1+<sub>intensity</sub>*FlipAngle<sub>nominal</sub> .                                                                                                                                                                                                                                                                                                                                                                    |
 | RF receive sensitivity map                   | RB1map    | In arbitrary units (arbitrary). Radio frequency (RF) receive (B1-) sensitivity maps are REQUIRED to use this suffix regardless of the method used to generate them. RB1map intensity values are RECOMMENDED to be represented as percent multiplicative factors such that Amplitude<sub>effective</sub> = B1-<sub>intensity</sub>*Amplitude<sub>ideal</sub>.                                                                                                                                                                                                                                                                                                                                                            |
 | Observed signal amplitude (S0) map           | S0map     | In arbitrary units (arbitrary). For a multi-echo (typically fMRI) sequence, S0 maps index the baseline signal before exponential (T2-star) signal decay. In other words: the exponential of the intercept for a linear decay model across log-transformed echos. For more information, please see, for example, [the tedana documentation](https://tedana.readthedocs.io/en/latest/approach.html#monoexponential-decay-model-fit). S0 maps are RECOMMENDED to use this suffix if derived from an ME-FMRI dataset. |
-| Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (arbitrary). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications (e.g. variable flip angle T1 mapping.                                                                                                                                                                                                                                          |
+| Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (arbitrary). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications (for example, variable flip angle T1 mapping.                                                                                                                                                                                                                                          |
 
 Parametric images listed in the table above are typically generated by
 processing a [file collection](../02-common-principles.md#entity-linked-file-collections).

From 244900dbed4aa2da3d2cfcff0b321b5c87bc0b50 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 4 Jan 2021 10:33:15 +0100
Subject: [PATCH 39/83] add missing newline at end of file

---
 src/schema/datatypes/anat.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/datatypes/anat.yaml b/src/schema/datatypes/anat.yaml
index 28e0c00897..2babef87a4 100644
--- a/src/schema/datatypes/anat.yaml
+++ b/src/schema/datatypes/anat.yaml
@@ -170,4 +170,4 @@
     ce: optional
     rec: optional
     mt: required
-    part: optional
\ No newline at end of file
+    part: optional

From 9d27efdbbab8cb0a24aecac75c0684f9d48813a4 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 4 Jan 2021 10:33:31 +0100
Subject: [PATCH 40/83] major syntax+linebreak overhaul qmri appendix

---
 src/99-appendices/11-qmri.md | 328 ++++++++++++++++++-----------------
 1 file changed, 170 insertions(+), 158 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 08e22ab239..0ded06d4ac 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -1,30 +1,37 @@
 # Appendix XI: Quantitative MRI
 
-Quantitative MRI (qMRI) is a collection of methods aiming at generating parametric
-maps that can characterize underlying tissue properties. Unlike that of conventional
-MR images (for example, `T1w`, `T2w`), intensity values of quantitative maps are not represented
-in an arbitrary grayscale range. Instead, these maps are represented either in absolute 
-physical units (for example, `seconds` for `T1map`), or within an application dependent range of
-arbitrary units (for example, myelin water fraction `MWFmap` in brain).
+Quantitative MRI (qMRI) is a collection of methods aiming at generating parametric maps
+that can characterize underlying tissue properties.
+Unlike that of conventional MR images (for example, `T1w`, `T2w`),
+intensity values of quantitative maps are not represented in an arbitrary grayscale range.
+Instead, these maps are represented either in absolute physical units
+(for example, `seconds` for `T1map`),
+or within an application dependent range of arbitrary units
+(for example, myelin water fraction `MWFmap` in brain).
 
 ## Organization of qMRI data in BIDS
 
-Unlike conventional MR images, quantitative maps are not immediate products of the
-image reconstruction step (from k-space data to structural images).
+Unlike conventional MR images, quantitative maps are not immediate products of the image reconstruction step
+(from k-space data to structural images).
 Intensity values of qMRI maps are calculated by fitting a collection of parametrically
-linked images to a biophysical model or to an MRI signal representation. This processing
-is typically carried out in the image domain.
+linked images to a biophysical model or to an MRI signal representation.
+This processing is typically carried out in the image domain.
 There are two main ways to obtain a quantitative map:
 
-1. Pre-generated qMRI maps: The qMRI maps are generated right after the reconstruction
-of required input images and made available to the user at the scanner console.
-The acquisition scenarios may include (a) vendor pipelines or (b) open-source pipelines
-deployed at the scanner site.
-
-2. Post-generated qMRI maps: The qMRI maps are generated from a collection of input
-data after they are exported from the scanner site. This type of processing is commonly
-carried out using an open-source software such as [hMRI toolbox](https://github.com/hMRI-group/hMRI-toolbox), [mrQ](https://github.com/mezera/mrQ), [PyQMRI](https://github.com/IMTtugraz/PyQMRI), [qmap](https://www.medphysics.wisc.edu/~samsonov/qmap/doc/qmap.html),
-[qMRLab](https://github.com/qmrlab/qmrlab) and [QUIT](https://github.com/spinicist/QUIT).
+1.  Pre-generated qMRI maps: The qMRI maps are generated right after the reconstruction
+    of required input images and made available to the user at the scanner console.
+    The acquisition scenarios may include (a) vendor pipelines or (b) open-source pipelines
+    deployed at the scanner site.
+
+2.  Post-generated qMRI maps: The qMRI maps are generated from a collection of input
+    data after they are exported from the scanner site.
+    This type of processing is commonly carried out using an open-source software such as
+    [hMRI toolbox](https://github.com/hMRI-group/hMRI-toolbox),
+    [mrQ](https://github.com/mezera/mrQ),
+    [PyQMRI](https://github.com/IMTtugraz/PyQMRI),
+    [qmap](https://www.medphysics.wisc.edu/~samsonov/qmap/doc/qmap.html),
+    [qMRLab](https://github.com/qmrlab/qmrlab),
+    and [QUIT](https://github.com/spinicist/QUIT).
 
 ### Inputs are file collections
 
@@ -33,8 +40,8 @@ application by creating logical groups of input files through `suffix` and certa
 representing acquisition parameters (`echo`, `flip`,`inv`, `mt`) or file parts (`part`).
 
 If a qMRI file collection is intended for creating structural quantitative maps (for example, `T1map`),
-files belonging to that collection are stored in the `anat` subfolder. Below is an example 
-file collection for `MP2RAGE`: 
+files belonging to that collection are stored in the `anat` subfolder.
+Below is an example file collection for `MP2RAGE`:
 
 ```text
 └── sub-01/
@@ -47,10 +54,10 @@ file collection for `MP2RAGE`:
          └── sub-01_inv-2_MP2RAGE.json
 ```
 
-Commonly, RF fieldmaps (`B1+` and `B1-` maps) are used for the correction of structural quantitative
-maps. As these images do not convey substantial structural information, respective file collections
-of RF fieldmaps are stored in the `fmap` subfolder. Below is an example file collection for RF transmit
-field map `TB1EPI`:
+Commonly, RF fieldmaps (`B1+` and `B1-` maps) are used for the correction of structural quantitative maps.
+As these images do not convey substantial structural information,
+respective file collections of RF fieldmaps are stored in the `fmap` subfolder.
+Below is an example file collection for RF transmit field map `TB1EPI`:
 
 ```text
 └── sub-01/
@@ -67,11 +74,12 @@ field map `TB1EPI`:
 
 Please visit the [file collections appendix](../99-appendices/10-file-collections.md#magnetic-resonance-imaging) to see the list of currently supported qMRI applications.
 
-### Quantitative maps are derivatives 
+### Quantitative maps are derivatives
+
+Regardless of how they are obtained (pre- or post-generated), qMRI maps are stored in the `derivatives` folder.
+For example a `T1map` can be generated from an `MP2RAGE` file collection using either options.
 
-Regardless of how they are obtained (pre- or post-generated), qMRI maps are stored in the
-`derivatives` folder. For example a `T1map` can be generated from an `MP2RAGE` file collection
-using either options. If the map is post-generated:
+If the map is post-generated:
 
 ```text
  ds-example/
@@ -99,10 +107,9 @@ If the map is pre-generated, for example, by a Siemens scanner:
                  └── sub-01_UNIT1.json
 ```
 
-Note: Even though the process from which pre-generated qMRI maps are obtained (vendor pipelines)
-is not known, vendors generally allow exporting of the corresponding input data. It is
-RECOMMENDED to share them along with the vendor outputs, whenever possible for a qMRI method
-supported by BIDS.
+Note: Even though the process from which pre-generated qMRI maps are obtained (vendor pipelines) is not known,
+vendors generally allow exporting of the corresponding input data.
+It is RECOMMENDED to share them along with the vendor outputs, whenever possible for a qMRI method supported by BIDS.
 
 ### Example datasets
 
@@ -110,9 +117,9 @@ You can find example file collections and qMRI maps organized according to BIDS
 
 ## Metadata requirements for qMRI data
 
-The table of required entities for qMRI file collections are provided in the [entity table](../99-appendices/04-entity-table.md). However,
-viability of a qMRI file collection is determined not only by the naming and organization of the
-input files, but also by which metadata fields are provided in accompanying json files.
+The table of required entities for qMRI file collections are provided in the [entity table](../99-appendices/04-entity-table.md).
+However, viability of a qMRI file collection is determined not only by the naming and organization of the input files,
+but also by which metadata fields are provided in accompanying json files.
 
 ### Method-specific priority levels for qMRI file collections
 
@@ -134,15 +141,16 @@ organization of `UNIT1` image.
 
 Explanation of the table:
 
-* The metadata fields listed in the REQUIRED column are needed to perform a minimum viable
-qMRI processing for the corresponding `file collection`.
-* Note that some of the metadata fields may be constant across different files in a file
-collection, yet still required as an input (for example, `NumberShots` in `MP2AGE`). Such metadata
-fields MUST be provided in the accompanying json files.
-* The metadata fields listed in the OPTIONAL column can be used to form different flavors
-of an existing file collection suffix, despensing with the need for introducing a new
-suffix. See [deriving the intended qMRI application from an ambiguos file collection](#Deriving-the-intended-qMRI-application-from-an-ambiguous-file-collection) section
-for details.
+*   The metadata fields listed in the REQUIRED column are needed to perform a minimum viable qMRI processing for the corresponding `file collection`.
+
+*   Note that some of the metadata fields may be constant across different files in a file collection,
+    yet still required as an input (for example, `NumberShots` in `MP2AGE`).
+    Such metadata fields MUST be provided in the accompanying json files.
+
+*   The metadata fields listed in the OPTIONAL column can be used to form different flavors of an existing file collection suffix,
+    dispensing with the need for introducing a new suffix.
+    See [deriving the intended qMRI application from an ambiguos file collection](#Deriving-the-intended-qMRI-application-from-an-ambiguous-file-collection)
+    for details.
 
 #### Field maps
 
@@ -160,10 +168,10 @@ for details.
 
 ### Meta-data requirements for qMRI maps
 
-As qMRI maps are stored as derivatives, they are subjected to the metadata requirements of 
+As qMRI maps are stored as derivatives, they are subjected to the metadata requirements of
 [derived datasets](03-modality-agnostic-files.html#derived-dataset-and-pipeline-description).
 
-An example `dataset_description.json` for a qMRI map derivatives folder: 
+An example `dataset_description.json` for a qMRI map derivatives folder:
 
 ```text
  ds-example/
@@ -178,7 +186,7 @@ An example `dataset_description.json` for a qMRI map derivatives folder:
                  └── sub-01_M0map.json
 ```
 
-dataset_description.json:
+`dataset_description.json`:
 
 ```text
 {
@@ -209,19 +217,17 @@ dataset_description.json:
 }
 ```
 
-In addition to the metadata fields provided in the `dataset_description.json`, qMRI maps
-are RECOMMENDED to be accompanied by sidecar JSON files that contain further information
-about the quantified maps. Although this may not be the generic case for common derivative
-outputs, a proper interpretation of qMRI maps may critically depend on some metadata
-fields. For example, without the information of `MagneticFieldStrength`, white-matter T1
-values in a `T1map` become elusive.
+In addition to the metadata fields provided in the `dataset_description.json`,
+qMRI maps are RECOMMENDED to be accompanied by sidecar JSON files that contain further information about the quantified maps.
+Although this may not be the generic case for common derivative outputs,
+a proper interpretation of qMRI maps may critically depend on some metadata fields.
+For example, without the information of `MagneticFieldStrength`, white-matter T1 values in a `T1map` become elusive.
 
-* All the acquisition parameters that are constant across the files in a file collection
-are RECOMMENDED to be added to the sidecar json of the qMRI maps.
-* Relevant acquisition parameters that vary across files in a qMRI file collection are
-RECOMMENDED to be added to the sidecar json of the qMRI map **`in array form`**.
-* The JSON file accompanying a qMRI map which is obtained by using open-source software
-is RECOMMENDED to include additional metadata fields listed in the following table:
+*   All the acquisition parameters that are constant across the files in a file collection are RECOMMENDED to be added to the sidecar json of the qMRI maps.
+
+*   Relevant acquisition parameters that vary across files in a qMRI file collection are RECOMMENDED to be added to the sidecar json of the qMRI map **in array form**.
+
+*   The JSON file accompanying a qMRI map which is obtained by using open-source software is RECOMMENDED to include additional metadata fields listed in the following table:
 
 | **Field name**                  | **Definition**                                                                                                               |
 | ------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- |
@@ -276,21 +282,21 @@ sub-01_T1map.json:
 
 ## Deriving the intended qMRI application from an ambiguous file collection
 
-Certain file colleciton suffixes may refer to a generic data collection regime such 
-as variable flip angle (VFA), rather than a more specific acquisition, for example,
-magnetization prepared two gradient echoes (MP2RAGE). Such generic acquisitions
-can serve as a basis to derive various qMRI applications by changes to the acquisition
-sequence (for example, readout) type or by varying additional scan parameters.
+Certain file colleciton suffixes may refer to a generic data collection regime such as variable flip angle (VFA),
+rather than a more specific acquisition, for example, magnetization prepared two gradient echoes (MP2RAGE).
+Such generic acquisitions can serve as a basis to derive various qMRI applications by changes to the acquisition sequence
+(for example, readout) type or by varying additional scan parameters.
 
-If such an inheritance relationship is applicable between an already existing file
-collection and a new qMRI application to be included in the specification, the inheritor
-qMRI method is listed in the table below instead of introducing a new file collection suffix.
+If such an inheritance relationship is applicable between an already existing file collection
+and a new qMRI application to be included in the specification,
+the inheritor qMRI method is listed in the table below instead of introducing a new file collection suffix.
 This approach aims at:
 
-* preventing the list of available suffixes from over-proliferation,
-* providing qMRI-focused BIDS applications with a set of meta-data driven rules to infer 
-possible fitting options,
-* keeping an inheritance track of the qMRI methods described within the specification.
+*   preventing the list of available suffixes from over-proliferation,
+
+*   providing qMRI-focused BIDS applications with a set of meta-data driven rules to infer possible fitting options,
+
+*   keeping an inheritance track of the qMRI methods described within the specification.
 
 | **File-collection suffix** | **If REQUIRED metadata == Value** | **OPTIONAL metadata [`entity`/`fixed`]**   | **Derived application name (NOT a suffix)** |
 |----------------------------|-----------------------------------|--------------------------------------------|---------------------------------------------|
@@ -318,7 +324,7 @@ in [this section](#Method-specific-priority-levels-for-qMRI-file-collections).
 For example, if the optional metadata field of `PulseSequenceType` is SPGR
 for a collection of anatomical images listed by the `VFA` suffix, the data
 qualifies for `DESPOT1` T1 fitting. For the same suffix, if the `PulseSequenceType`
-metadata field has the value of `SSFP`, and the `SpoilingRFPhaseIncrement` is 
+metadata field has the value of `SSFP`, and the `SpoilingRFPhaseIncrement` is
 provided as a metadata field, then the dataset becomes eligible for `DESPOT2`
 T2 fitting application.
 
@@ -329,20 +335,25 @@ column of [the priority levels table](#Method-specific-priority-levels-for-qMRI-
 ## Introducing a new qMRI file collection
 
 If a qMRI application can not be interpreted as subset of an already existing suffix
-of a qMRI-related file collection, we RECOMMEND adhering to the following principles to 
+of a qMRI-related file collection, we RECOMMEND adhering to the following principles to
 introduce a new suffix:
 
-* All qMRI-relevant file collection suffixes are capitalized.
-* Unless the pulse sequence is exclusively associated with a specific qMRI application
-(for example, `MP2RAGE`), sequence names are not used as suffixes.
-* File collection suffixes for qMRI applications attain a clear description
-of the qMRI method that they relate to in the [file collections appendix]((../99-appendices/10-file-collections.md#magnetic-resonance-imaging)).
-* Hyperlinks to example applications and reference method articles are encouraged
-whenever possible.
-* If it is possible to derive a qMRI application from an already existing file collection
-suffix by defining a set of logical conditions over the metadata fields, the tables of
-[deriving the intended qMRI application from an ambiguous file collection](#Deriving-the-intended-qMRI-application-from-an-ambiguous-file-collection) and the
-[anatomy data priority levels](#Anatomy-imaging-data) sections are extended instead of introducing a new suffix.
+*   All qMRI-relevant file collection suffixes are capitalized.
+
+*   Unless the pulse sequence is exclusively associated with a specific qMRI application
+    (for example, `MP2RAGE`), sequence names are not used as suffixes.
+
+*   File collection suffixes for qMRI applications attain a clear description of the qMRI method that they relate to in the
+    [file collections appendix]((../99-appendices/10-file-collections.md#magnetic-resonance-imaging)).
+
+*   Hyperlinks to example applications and reference method articles are encouraged whenever possible.
+
+*   If it is possible to derive a qMRI application from an already existing file collection suffix
+    by defining a set of logical conditions over the metadata fields, the tables of the
+    [deriving the intended qMRI application from an ambiguous file collection](#Deriving-the-intended-qMRI-application-from-an-ambiguous-file-collection)
+    and the
+    [anatomy data priority levels](#Anatomy-imaging-data)
+    sections are extended instead of introducing a new suffix.
 
 ## Application-specific notes for qMRI file collections
 
@@ -350,10 +361,10 @@ suffix by defining a set of logical conditions over the metadata fields, the tab
 
 General notes:
 
-* Some BIDS metadata field values are calculated based on the values of other metadata fields
-that are not listed as required fields. These fields include: `NumberShots`. The calculation of
-the values may depend on the type of the acquisition. These acquisitions include: `MP2RAGE` and 
-`TB1SRGE`. 
+*   Some BIDS metadata field values are calculated based on the values of other metadata fields that are not listed as required fields.
+    These fields include: `NumberShots`.
+    The calculation of the values may depend on the type of the acquisition.
+    These acquisitions include: `MP2RAGE` and `TB1SRGE`.
 
 #### `MP2RAGE` specific notes
 
@@ -367,46 +378,49 @@ see the relevant discussion [here](https://github.com/qMRLab/qMRLab/issues/255).
 
 Therefore, the `UNIT1` image provided by the scanner is RECOMMENDED to be stored under the `anat`
 raw dataset directory along with the `MP2RAGE` file collection and to be used as the primary input
-for quantifying a `T1map`. 
+for quantifying a `T1map`.
 
-If an additional `UNIT1` image is calculated offline, then the output is to be stored in the 
+If an additional `UNIT1` image is calculated offline, then the output is to be stored in the
 `derivatives` folder with neccesary provenance information.
 
-##### `NumberShots` metadata field 
+##### `NumberShots` metadata field
 
 Note that type of `NumberShots` field can be either a `number` or an `array of numbers`.
 
-* If a single `number` is to be provided, this should correspond to the number of `SlicesPerSlab` or 
-`ReconMatrixPE`. However, in this case, `SlicePartialFourier` or `PartialFourierPE` fraction is needed
-to calculate the number of partitions `before` and `after` of the k-space center to calculate a T1 map.
-* If `before/after` calculation is performed during the BIDS conversion of the `MP2RAGE` data, then
-then the value of `NumberShots` metadata field can be given as a 1X2 array, with first entry corresponding
-to `before` and the second to the `after`.
+*   If a single `number` is to be provided, this should correspond to the number of `SlicesPerSlab` or `ReconMatrixPE`.
+    However, in this case, `SlicePartialFourier` or `PartialFourierPE` fraction is needed
+    to calculate the number of partitions `before` and `after` of the k-space center to calculate a T1 map.
+
+*   If `before/after` calculation is performed during the BIDS conversion of the `MP2RAGE` data,
+    then the value of `NumberShots` metadata field can be given as a 1X2 array,
+    with first entry corresponding to `before` and the second to the `after`.
 
 Formula:
 
-If NumberShots is an array of numbers such that `"NumberShots": [before, after]`, the values of
-`before` and `after` are calculated as follows ([reference](https://github.com/JosePMarques/MP2RAGE-related-scripts/blob/a405df30ac2c617d29d8b1b16025aaa911e86370/func/bids_T1B1correct.m#L16)):
+If NumberShots is an array of numbers such that `"NumberShots": [before, after]`,
+the values of `before` and `after` are calculated as follows:
 
 ```text
 before = SlicesPerSlab*(SlicePartialFourier - 0.5)
 after  = SlicesPerSlab/2
 ```
 
+See this [reference](https://github.com/JosePMarques/MP2RAGE-related-scripts/blob/a405df30ac2c617d29d8b1b16025aaa911e86370/func/bids_T1B1correct.m#L16).
+
 ##### Other metadata fields
 
-The value of the `RepetitionTimeExcitation` is not commonly found in the DICOM files. When
-accessible, the value of `EchoSpacing` corresponds to this metadata. When not accessible,
-`2 X EchoTime` can be used as a surrogate.
+The value of the `RepetitionTimeExcitation` is not commonly found in the DICOM files.
+When accessible, the value of `EchoSpacing` corresponds to this metadata.
+When not accessible, `2 X EchoTime` can be used as a surrogate.
 
 Further information about other `MP2RAGE` qMRI protocol fields can be found [here](https://qmrlab.readthedocs.io/en/master/protocols.html#mp2rage).
 
 #### `TB1SRGE` specific notes
 
-Calculation of `before` and `after` entries for `NumberShots` metadata field of `TB1SRGE`
-is more involved than that of `MP2RAGE`. The formula can be found [here](https://github.com/JosePMarques/MP2RAGE-related-scripts/blob/a405df30ac2c617d29d8b1b16025aaa911e86370/DemoForR1Correction.m#L17), which requires 
-information about `BaseResolution` (that is, image matrix size in PE direction), partial Fourier
-fraction in the PE direction, number of reference lines for parallel imaging acceleration
+Calculation of `before` and `after` entries for `NumberShots` metadata field of `TB1SRGE` is more involved than that of `MP2RAGE`.
+The formula can be found [here](https://github.com/JosePMarques/MP2RAGE-related-scripts/blob/a405df30ac2c617d29d8b1b16025aaa911e86370/DemoForR1Correction.m#L17),
+which requires information about `BaseResolution` (that is, image matrix size in PE direction),
+partial Fourier fraction in the PE direction, number of reference lines for parallel imaging acceleration,
 and the parallel imaging acceleration factor in PE direction.
 
 
@@ -414,12 +428,12 @@ and the parallel imaging acceleration factor in PE direction.
 
 General notes:
 
-* Some RF file collections call for the use of special notations that cannot be resolved by
-by entities that can generalize to other applications. Instead of introducing an entity
-that is exclusive to a single application, method developers who commonly use these file
-collections for the `MPM` application reached the consensus on the use of `acq` entity to
-distinguish individual files. These suffixes include: `TB1AFI`, `TB1TFL`, `TB1RMF` and
-`RB1COR`.
+*   Some RF file collections call for the use of special notations that cannot be resolved by
+    by entities that can generalize to other applications.
+    Instead of introducing an entity that is exclusive to a single application,
+    method developers who commonly use these file collections for the `MPM` application reached
+    the consensus on the use of `acq` entity to distinguish individual files.
+    These suffixes include: `TB1AFI`, `TB1TFL`, `TB1RMF`, and `RB1COR`.
 
 #### `TB1EPI` specific notes
 
@@ -427,30 +441,30 @@ The `flip` and `echo` entities MUST be used to distinguish images with this suff
 The use of `flip` follows the default convention. However, this suffix defines a
 specific use case for the `echo` entity:
 
-|`echo-1`|`echo-2`|
-|:--|:----|
-|Lower `EchoTime` | Higher `EchoTime`                  |
-|Spin Echo (SE) image|Stimulated Echo (STE) image|
+| `echo-1`             |`echo-2`                     |
+| -------------------- | --------------------------- |
+| Lower `EchoTime`     | Higher `EchoTime`           |
+| Spin Echo (SE) image | Stimulated Echo (STE) image |
 
 At each `FlipAngle`, the `TB1EPI` suffix lists two images acquired at two echo times.
-The first echo is a spin echo (SE) formed by the pulses alpha-2alpha. However, the 
+The first echo is a spin echo (SE) formed by the pulses alpha-2alpha. However, the
 second echo in this method is generated in a different fashion compared to a typical
-MESE acquisition. The second echo is a stimulated echo (STE) that is formed by an 
+MESE acquisition. The second echo is a stimulated echo (STE) that is formed by an
 additional alpha pulse (that is, alpha-2alpha-alpha).
 
 The `FlipAngle` value corresponds to the nominal flip angle value of the STE pulse.
 The nominal FA value of the SE pulse is twice this value.
 
-Note that the following metadata fields MUST be defined in the accompanying JSON 
+Note that the following metadata fields MUST be defined in the accompanying JSON
 files:
 
-| Field name         | Definition |
-| :----------------- | :--------- |
-| `TotalReadoutTime` |   The effective readout length defined as `EffectiveEchoSpacing * PEReconMatrix`, with `EffectiveEchoSpacing = TrueEchoSpacing / PEacceleration`         |
-| `MixingTime`       |  Time interval between the SE and STE pulses          |
+| Field name         | Definition                                                                                                                                      |
+| ------------------ | ----------------------------------------------------------------------------------------------------------------------------------------------- |
+| `TotalReadoutTime` |  The effective readout length defined as `EffectiveEchoSpacing * PEReconMatrix`, with `EffectiveEchoSpacing = TrueEchoSpacing / PEacceleration` |
+| `MixingTime`       |  Time interval between the SE and STE pulses                                                                                                    |
 
 To properly identify constituents of this particular method, values of the `echo`
-entity MUST index the images as follows:  
+entity MUST index the images as follows:
 
 ```text
 └── sub-01/
@@ -467,21 +481,20 @@ entity MUST index the images as follows:
 
 #### `TB1AFI` specific notes
 
-This method calculates a B1<sup>+</sup> map from two images acquired at two
-interleaved excitation repetition times (TR). Note that there is no entity 
-for the TR that can be used to label the files corresponding to the two
+This method calculates a B1<sup>+</sup> map from two images acquired at two interleaved excitation repetition times (TR).
+Note that there is no entity for the TR that can be used to label the files corresponding to the two
 repetition times and the definition of repetition time depends on the modality
-(`functional` or `anatomical`) in the specification. 
+(`functional` or `anatomical`) in the specification.
 
-Therefore, to properly identify constituents of this particular method, values of 
-the `acq` entity SHOULD begin with either `tr1` (lower TR) or `tr2` (higher TR) 
-and MAY be followed by freeform entries:  
+Therefore, to properly identify constituents of this particular method,
+values of the `acq` entity SHOULD begin with either `tr1` (lower TR) or `tr2` (higher TR)
+and MAY be followed by freeform entries:
 
-|First `TR`|Second `TR`|Use case|
-|:--|:----| :----| 
-|`_acq-tr1`|`_acq-tr2`|Single acquisition|
-|`_acq-tr1Test`|`_acq-tr2Test`|Acquisition `Test`|
-|`_acq-tr1Retest`|`_acq-tr2Retest`|Acquisition `Retest`|
+| First `TR`       | Second `TR`      | Use case             |
+| ---------------- | ---------------- | -------------------- |
+| `_acq-tr1`       | `_acq-tr2`       | Single acquisition   |
+| `_acq-tr1Test`   | `_acq-tr2Test`   | Acquisition `Test`   |
+| `_acq-tr1Retest` | `_acq-tr2Retest` | Acquisition `Retest` |
 
 ```text
 └── sub-01/
@@ -494,30 +507,29 @@ and MAY be followed by freeform entries:
 
 #### `TB1TFL` and `TB1RMF` specific notes
 
-These suffixes describe two outputs generated by Siemens `tfl_b1_map` and `rf_map`
-product sequences, respectively. Both sequences output two images. The first image
-appears like an anatomical image and the second output is a scaled flip angle map.
+These suffixes describe two outputs generated by Siemens `tfl_b1_map` and `rf_map` product sequences, respectively.
+Both sequences output two images.
+The first image appears like an anatomical image and the second output is a scaled flip angle map.
 
-To properly identify files of this particular file collection, values of 
-the `acq` entity SHOULD begin with either `anat` or `famp` and MAY be followed 
-by freeform entries:
+To properly identify files of this particular file collection,
+values of the `acq` entity SHOULD begin with either `anat` or `famp` and MAY be followed by freeform entries:
 
-|Anatomical (like) image|Scaled FA map|Use case|
-|:--|:----| :----| 
-|`_acq-anat`|`_acq-famp`|Single acquisition|
-|`_acq-anatTest`|`_acq-fampTest`|Acquisition `Test`|
-|`_acq-anatRetest`|`_acq-fampRetest`|Acquisition `Retest`|
+| Anatomical (like) image |Scaled FA map      |Use case              |
+| ----------------------- | ----------------- | -------------------- |
+| `_acq-anat`             | `_acq-famp`       | Single acquisition   |
+| `_acq-anatTest`         | `_acq-fampTest`   | Acquisition `Test`   |
+| `_acq-anatRetest`       | `_acq-fampRetest` | Acquisition `Retest` |
 
 ```text
 └── sub-01/
      └── fmap/
-         ├── sub-01_acq-anat_TB1TFL.nii.gz 
+         ├── sub-01_acq-anat_TB1TFL.nii.gz
          ├── sub-01_acq-anat_TB1TFL.json
          ├── sub-01_acq-famp_TB1TFL.nii.gz
          └── sub-01_acq-famp_TB1TFL.json
 ```
 
-The example above applies to the `TB1RFM` suffix as well. 
+The example above applies to the `TB1RFM` suffix as well.
 
 #### `RB1COR` specific notes
 
@@ -527,14 +539,14 @@ with identical acquisition parameters.
 
 To properly identify constituents of this particular method, values of the `acq`
 entity SHOULD begin with either `body` or `head` and MAY be followed by freeform
-entries:  
-
-|Body coil|Head coil|Use case|
-|:--|:----| :----| 
-|`_acq-body`|`_acq-head`|Single acquisition|
-|`_acq-bodyMTw`|`_acq-headMTw`|`MTw` for `MPM`|
-|`_acq-bodyPDw`|`_acq-headPDw`|`PDw` for `MPM`|
-|`_acq-bodyT1w`|`_acq-headT1w`|`T1w` for `MPM`|
+entries:
+
+| Body coil      | Head coil      | Use case           |
+| -------------- | -------------- | ------------------ |
+| `_acq-body`    | `_acq-head`    | Single acquisition |
+| `_acq-bodyMTw` | `_acq-headMTw` | `MTw` for `MPM`    |
+| `_acq-bodyPDw` | `_acq-headPDw` | `PDw` for `MPM`    |
+| `_acq-bodyT1w` | `_acq-headT1w` | `T1w` for `MPM`    |
 
 ```text
 └── sub-01/

From cb9738cf19444a0a11177615db191225a5a862f5 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 4 Jan 2021 10:40:39 +0100
Subject: [PATCH 41/83] remaining qmri appendix syntax issues, except one to be
 discussed

---
 src/99-appendices/11-qmri.md | 44 ++++++++++++++++++------------------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 0ded06d4ac..f6fd5636a0 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -23,7 +23,7 @@ There are two main ways to obtain a quantitative map:
     The acquisition scenarios may include (a) vendor pipelines or (b) open-source pipelines
     deployed at the scanner site.
 
-2.  Post-generated qMRI maps: The qMRI maps are generated from a collection of input
+1.  Post-generated qMRI maps: The qMRI maps are generated from a collection of input
     data after they are exported from the scanner site.
     This type of processing is commonly carried out using an open-source software such as
     [hMRI toolbox](https://github.com/hMRI-group/hMRI-toolbox),
@@ -141,13 +141,13 @@ organization of `UNIT1` image.
 
 Explanation of the table:
 
-*   The metadata fields listed in the REQUIRED column are needed to perform a minimum viable qMRI processing for the corresponding `file collection`.
+-   The metadata fields listed in the REQUIRED column are needed to perform a minimum viable qMRI processing for the corresponding `file collection`.
 
-*   Note that some of the metadata fields may be constant across different files in a file collection,
+-   Note that some of the metadata fields may be constant across different files in a file collection,
     yet still required as an input (for example, `NumberShots` in `MP2AGE`).
     Such metadata fields MUST be provided in the accompanying json files.
 
-*   The metadata fields listed in the OPTIONAL column can be used to form different flavors of an existing file collection suffix,
+-   The metadata fields listed in the OPTIONAL column can be used to form different flavors of an existing file collection suffix,
     dispensing with the need for introducing a new suffix.
     See [deriving the intended qMRI application from an ambiguos file collection](#Deriving-the-intended-qMRI-application-from-an-ambiguous-file-collection)
     for details.
@@ -223,11 +223,14 @@ Although this may not be the generic case for common derivative outputs,
 a proper interpretation of qMRI maps may critically depend on some metadata fields.
 For example, without the information of `MagneticFieldStrength`, white-matter T1 values in a `T1map` become elusive.
 
-*   All the acquisition parameters that are constant across the files in a file collection are RECOMMENDED to be added to the sidecar json of the qMRI maps.
+-   All the acquisition parameters that are constant across the files in a file collection are RECOMMENDED
+    to be added to the sidecar json of the qMRI maps.
 
-*   Relevant acquisition parameters that vary across files in a qMRI file collection are RECOMMENDED to be added to the sidecar json of the qMRI map **in array form**.
+-   Relevant acquisition parameters that vary across files in a qMRI file collection are RECOMMENDED
+    to be added to the sidecar json of the qMRI map **in array form**.
 
-*   The JSON file accompanying a qMRI map which is obtained by using open-source software is RECOMMENDED to include additional metadata fields listed in the following table:
+-   The JSON file accompanying a qMRI map which is obtained by using open-source software is RECOMMENDED
+    to include additional metadata fields listed in the following table:
 
 | **Field name**                  | **Definition**                                                                                                               |
 | ------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- |
@@ -292,11 +295,9 @@ and a new qMRI application to be included in the specification,
 the inheritor qMRI method is listed in the table below instead of introducing a new file collection suffix.
 This approach aims at:
 
-*   preventing the list of available suffixes from over-proliferation,
-
-*   providing qMRI-focused BIDS applications with a set of meta-data driven rules to infer possible fitting options,
-
-*   keeping an inheritance track of the qMRI methods described within the specification.
+-   preventing the list of available suffixes from over-proliferation,
+-   providing qMRI-focused BIDS applications with a set of meta-data driven rules to infer possible fitting options,
+-   keeping an inheritance track of the qMRI methods described within the specification.
 
 | **File-collection suffix** | **If REQUIRED metadata == Value** | **OPTIONAL metadata [`entity`/`fixed`]**   | **Derived application name (NOT a suffix)** |
 |----------------------------|-----------------------------------|--------------------------------------------|---------------------------------------------|
@@ -338,17 +339,17 @@ If a qMRI application can not be interpreted as subset of an already existing su
 of a qMRI-related file collection, we RECOMMEND adhering to the following principles to
 introduce a new suffix:
 
-*   All qMRI-relevant file collection suffixes are capitalized.
+-   All qMRI-relevant file collection suffixes are capitalized.
 
-*   Unless the pulse sequence is exclusively associated with a specific qMRI application
+-   Unless the pulse sequence is exclusively associated with a specific qMRI application
     (for example, `MP2RAGE`), sequence names are not used as suffixes.
 
-*   File collection suffixes for qMRI applications attain a clear description of the qMRI method that they relate to in the
+-   File collection suffixes for qMRI applications attain a clear description of the qMRI method that they relate to in the
     [file collections appendix]((../99-appendices/10-file-collections.md#magnetic-resonance-imaging)).
 
-*   Hyperlinks to example applications and reference method articles are encouraged whenever possible.
+-   Hyperlinks to example applications and reference method articles are encouraged whenever possible.
 
-*   If it is possible to derive a qMRI application from an already existing file collection suffix
+-   If it is possible to derive a qMRI application from an already existing file collection suffix
     by defining a set of logical conditions over the metadata fields, the tables of the
     [deriving the intended qMRI application from an ambiguous file collection](#Deriving-the-intended-qMRI-application-from-an-ambiguous-file-collection)
     and the
@@ -361,7 +362,7 @@ introduce a new suffix:
 
 General notes:
 
-*   Some BIDS metadata field values are calculated based on the values of other metadata fields that are not listed as required fields.
+-   Some BIDS metadata field values are calculated based on the values of other metadata fields that are not listed as required fields.
     These fields include: `NumberShots`.
     The calculation of the values may depend on the type of the acquisition.
     These acquisitions include: `MP2RAGE` and `TB1SRGE`.
@@ -387,11 +388,11 @@ If an additional `UNIT1` image is calculated offline, then the output is to be s
 
 Note that type of `NumberShots` field can be either a `number` or an `array of numbers`.
 
-*   If a single `number` is to be provided, this should correspond to the number of `SlicesPerSlab` or `ReconMatrixPE`.
+-   If a single `number` is to be provided, this should correspond to the number of `SlicesPerSlab` or `ReconMatrixPE`.
     However, in this case, `SlicePartialFourier` or `PartialFourierPE` fraction is needed
     to calculate the number of partitions `before` and `after` of the k-space center to calculate a T1 map.
 
-*   If `before/after` calculation is performed during the BIDS conversion of the `MP2RAGE` data,
+-   If `before/after` calculation is performed during the BIDS conversion of the `MP2RAGE` data,
     then the value of `NumberShots` metadata field can be given as a 1X2 array,
     with first entry corresponding to `before` and the second to the `after`.
 
@@ -423,12 +424,11 @@ which requires information about `BaseResolution` (that is, image matrix size in
 partial Fourier fraction in the PE direction, number of reference lines for parallel imaging acceleration,
 and the parallel imaging acceleration factor in PE direction.
 
-
 ### Radiofrequency (RF) field mapping
 
 General notes:
 
-*   Some RF file collections call for the use of special notations that cannot be resolved by
+-   Some RF file collections call for the use of special notations that cannot be resolved by
     by entities that can generalize to other applications.
     Instead of introducing an entity that is exclusive to a single application,
     method developers who commonly use these file collections for the `MPM` application reached

From d7d760407b2ea89186eaa8bebdbdc5010febaccc Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 4 Jan 2021 10:42:14 +0100
Subject: [PATCH 42/83] fix table pipes in 10-file-collections.md

---
 src/99-appendices/10-file-collections.md | 32 ++++++++++++------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/src/99-appendices/10-file-collections.md b/src/99-appendices/10-file-collections.md
index 37645aca9e..eb260f0e56 100644
--- a/src/99-appendices/10-file-collections.md
+++ b/src/99-appendices/10-file-collections.md
@@ -30,15 +30,15 @@ sub-<label>/[ses-<label>/]
         sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>][_flip-<index>][_inv-<index>][_mt-<label>][_part-<label>]_<suffix>.nii[.gz]
 ```
 
-| Suffix  | Linking entities      | Application                                | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
-|---------|-----------------------|--------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| VFA     | flip                  | Variable flip angle                        | The VFA method involves at least two spoiled gradient echo (SPGR) of steady-state free precession (SSFP) images acquired at different flip angles. Depending on the provided metadata fields and the sequence type, data may be eligible for DESPOT1, DESPOT2 and their variants ([Deoni et al. 2005](https://doi.org/10.1002/mrm.20314)).                                                                                           |
-| IRT1    | inv, part             | Inversion recovery T1 mapping              | The IRT1 method involves multiple inversion recovery spin-echo images acquired at different inversion times ([Barral et al. 2010](https://doi.org/10.1002/mrm.22497)).                                                                                                                                                                                                                                                               |
-| MP2RAGE | flip, inv, echo, part | Magnetization prepared two gradient echoes | The MP2RAGE method is a special protocol that collects several images at different flip angles and inversion times to create a parametric T1map by combining the magnitude and phase images ([Marques et al. 2010](https://doi.org/10.1016/j.neuroimage.2009.10.002)).                                                               |
-| MESE    | echo                  | Multi-echo spin-echo                       | The MESE method involves multiple spin echo images acquired at different echo times and is primarily used for T2 mapping. Please note that this suffix is not intended for the logical grouping of images acquired using an Echo Planar Imaging (EPI) readout.                                                                                                                                                                                                |
-| MEGRE   | echo                  | Multi-echo gradient-echo                   | Anatomical gradient echo images acquired at different echo times. Please note that this suffix is not intended for the logical grouping of images acquired using an Echo Planar Imaging (EPI) readout.                                                                                                                                                                                                                                                        |
-| MTR     | mt                    | Magnetization transfer ratio               | This method is to calculate a semi-quantitative magnetization transfer ratio map.                                                                                                                                                                                                                                                                                                                                                                             |
-| MTS     | flip, mt              | Magnetization transfer saturation          | This method is to calculate a semi-quantitative magnetization transfer saturation index map. The MTS method involves three sets of anatomical images that differ in terms of application of a magnetization transfer RF pulse (MTon or MToff) and flip angle ([Helms et al. 2008](https://doi.org/10.1002/mrm.21732)).                                                                                                               |
+| Suffix  | Linking entities      | Application                                | Description                                                                                                                                                                                                                                                                                                                                                                                                                         |
+|---------|-----------------------|--------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| VFA     | flip                  | Variable flip angle                        | The VFA method involves at least two spoiled gradient echo (SPGR) of steady-state free precession (SSFP) images acquired at different flip angles. Depending on the provided metadata fields and the sequence type, data may be eligible for DESPOT1, DESPOT2 and their variants ([Deoni et al. 2005](https://doi.org/10.1002/mrm.20314)).                                                                                          |
+| IRT1    | inv, part             | Inversion recovery T1 mapping              | The IRT1 method involves multiple inversion recovery spin-echo images acquired at different inversion times ([Barral et al. 2010](https://doi.org/10.1002/mrm.22497)).                                                                                                                                                                                                                                                              |
+| MP2RAGE | flip, inv, echo, part | Magnetization prepared two gradient echoes | The MP2RAGE method is a special protocol that collects several images at different flip angles and inversion times to create a parametric T1map by combining the magnitude and phase images ([Marques et al. 2010](https://doi.org/10.1016/j.neuroimage.2009.10.002)).                                                                                                                                                              |
+| MESE    | echo                  | Multi-echo spin-echo                       | The MESE method involves multiple spin echo images acquired at different echo times and is primarily used for T2 mapping. Please note that this suffix is not intended for the logical grouping of images acquired using an Echo Planar Imaging (EPI) readout.                                                                                                                                                                      |
+| MEGRE   | echo                  | Multi-echo gradient-echo                   | Anatomical gradient echo images acquired at different echo times. Please note that this suffix is not intended for the logical grouping of images acquired using an Echo Planar Imaging (EPI) readout.                                                                                                                                                                                                                              |
+| MTR     | mt                    | Magnetization transfer ratio               | This method is to calculate a semi-quantitative magnetization transfer ratio map.                                                                                                                                                                                                                                                                                                                                                   |
+| MTS     | flip, mt              | Magnetization transfer saturation          | This method is to calculate a semi-quantitative magnetization transfer saturation index map. The MTS method involves three sets of anatomical images that differ in terms of application of a magnetization transfer RF pulse (MTon or MToff) and flip angle ([Helms et al. 2008](https://doi.org/10.1002/mrm.21732)).                                                                                                              |
 | MPM     | flip, mt, echo, part  | Multi-parametric mapping                   | The MPM approaches (a.k.a hMRI) involves the acquisition of highly-similar anatomical images that differ in terms of application of a magnetization transfer RF pulse (MTon or MToff), flip angle and (optionally) echo time and magnitue/phase parts ([Weiskopf et al. 2013](https://doi.org/10.3389/fnins.2013.00095)). See [here](https://owncloud.gwdg.de/index.php/s/iv2TOQwGy4FGDDZ) for suggested MPM acquisition protocols. |
 
 ### Fieldmap data
@@ -49,12 +49,12 @@ sub-<label>/[ses-<label>/]
         sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>][_flip-<index>][_inv-<index>][_mt-<label>][_part-<label>]_<suffix>.nii[.gz]
 ```
 
-| Suffix  | Meta-data relevant entity                                    | Application                        | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
-|---------|--------------------------------------------------------------|------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| TB1DAM  | flip                                                         | Double-angle B1+ mapping           | The double-angle B1<sup>+</sup> method ([Insko and Bolinger 1993](https://doi.org/10.1006/jmra.1993.1133)) is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation flip angles. Common sequence types for this application include spin echo and echo planar imaging.                                                                                                |
-| TB1EPI  | flip, echo                                                   | B1<sup>+</sup> mapping with 3D EPI | This B1<sup>+</sup> mapping method ([Jiru and Klose 2006](https://doi.org/10.1002/mrm.21083)) is based on two EPI readouts to acquire spin echo (SE) and stimulated echo (STE) images at multiple flip angles in one sequence, used in the calculation of deviations from the nominal flip angle.                                                                                                                                                                             |
-| TB1AFI  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Actual Flip Angle Imaging (AFI)    | This method ([Yarnykh 2007](https://doi.org/10.1002/mrm.21120)) calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence.                                                                                                                                                                                                                                                                      |
+| Suffix  | Meta-data relevant entity                                    | Application                        | Description                                                                                                                                                                                                                                                                                                                                                                                                                                             |
+|---------|--------------------------------------------------------------|------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| TB1DAM  | flip                                                         | Double-angle B1+ mapping           | The double-angle B1<sup>+</sup> method ([Insko and Bolinger 1993](https://doi.org/10.1006/jmra.1993.1133)) is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation flip angles. Common sequence types for this application include spin echo and echo planar imaging.                                                                                                        |
+| TB1EPI  | flip, echo                                                   | B1<sup>+</sup> mapping with 3D EPI | This B1<sup>+</sup> mapping method ([Jiru and Klose 2006](https://doi.org/10.1002/mrm.21083)) is based on two EPI readouts to acquire spin echo (SE) and stimulated echo (STE) images at multiple flip angles in one sequence, used in the calculation of deviations from the nominal flip angle.                                                                                                                                                       |
+| TB1AFI  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Actual Flip Angle Imaging (AFI)    | This method ([Yarnykh 2007](https://doi.org/10.1002/mrm.21120)) calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence.                                                                                                                                                                                                                                               |
 | TB1TFL  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `tfl_b1_map`               | B1<sup>+</sup> data acquired using `tfl_b1_map` product sequence by Siemens based on the method by [Chung et al. (2010)](https://doi.org/10.1002/mrm.22423). The sequence generates one anatomical image and one scaled flip angle map.                                                                                                                                                                                                                 |
-| TB1RMF  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `rf_map`                   | B1<sup>+</sup> data acquired using `rf_map` product sequence by Siemens.                                                                                                                                                                                                                                                                                                                                                                                                          |
+| TB1RMF  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `rf_map`                   | B1<sup>+</sup> data acquired using `rf_map` product sequence by Siemens.                                                                                                                                                                                                                                                                                                                                                                                |
 | TB1SRGE | `flip`, `inv`                                                | SA2RAGE                            | Saturation-prepared with 2 rapid gradient echoes (SA2RAGE) uses a ratio of two saturation recovery images with different time delays, and a simulated look-up table to estimate B1+ ([Eggenschwiler et al. 2011](https://doi.org/10.1002/mrm.23145)). This sequence can also be used in conjunction with MP2RAGE T1 mapping to iteratively improve B1+ and T1 map estimation ([Marques & Gruetter 2013](https://doi.org/10.1371/journal.pone.0069294)). |
-| RB1COR  | Please see the [qMRI appendix](../99-appendices/11-qmri.md).  | B1<sup>-</sup> field correction    | Low resolution images acquired by the body coil (in the gantry of the scanner) and the head coil using identical acquisition parameters to generate a combined sensitivity map as described in [Papp et al. (2016)](https://doi.org/10.1002/mrm.26058).                                                                                                                                                                                                  |
+| RB1COR  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | B1<sup>-</sup> field correction    | Low resolution images acquired by the body coil (in the gantry of the scanner) and the head coil using identical acquisition parameters to generate a combined sensitivity map as described in [Papp et al. (2016)](https://doi.org/10.1002/mrm.26058).                                                                                                                                                                                                 |

From b9c2ef5dfee49d8870d3f228f458444e47cbed40 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 4 Jan 2021 10:47:07 +0100
Subject: [PATCH 43/83] fix ill-formatted links

---
 src/99-appendices/11-qmri.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index f6fd5636a0..bb4b4cee95 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -72,7 +72,7 @@ Below is an example file collection for RF transmit field map `TB1EPI`:
          └── sub-01_fa-2_echo-2_TB1EPI.json
 ```
 
-Please visit the [file collections appendix](../99-appendices/10-file-collections.md#magnetic-resonance-imaging) to see the list of currently supported qMRI applications.
+Please visit the [file collections appendix](./10-file-collections.md#magnetic-resonance-imaging) to see the list of currently supported qMRI applications.
 
 ### Quantitative maps are derivatives
 
@@ -169,7 +169,7 @@ Explanation of the table:
 ### Meta-data requirements for qMRI maps
 
 As qMRI maps are stored as derivatives, they are subjected to the metadata requirements of
-[derived datasets](03-modality-agnostic-files.html#derived-dataset-and-pipeline-description).
+[derived datasets](../03-modality-agnostic-files.md#derived-dataset-and-pipeline-description).
 
 An example `dataset_description.json` for a qMRI map derivatives folder:
 
@@ -441,7 +441,7 @@ The `flip` and `echo` entities MUST be used to distinguish images with this suff
 The use of `flip` follows the default convention. However, this suffix defines a
 specific use case for the `echo` entity:
 
-| `echo-1`             |`echo-2`                     |
+| `echo-1`             | `echo-2`                    |
 | -------------------- | --------------------------- |
 | Lower `EchoTime`     | Higher `EchoTime`           |
 | Spin Echo (SE) image | Stimulated Echo (STE) image |
@@ -514,7 +514,7 @@ The first image appears like an anatomical image and the second output is a scal
 To properly identify files of this particular file collection,
 values of the `acq` entity SHOULD begin with either `anat` or `famp` and MAY be followed by freeform entries:
 
-| Anatomical (like) image |Scaled FA map      |Use case              |
+| Anatomical (like) image | Scaled FA map     | Use case             |
 | ----------------------- | ----------------- | -------------------- |
 | `_acq-anat`             | `_acq-famp`       | Single acquisition   |
 | `_acq-anatTest`         | `_acq-fampTest`   | Acquisition `Test`   |

From 80cd25ecc2c56d40407e860bb8376ec18a646d13 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 4 Jan 2021 10:51:01 +0100
Subject: [PATCH 44/83] some more link fixes

---
 src/99-appendices/11-qmri.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index bb4b4cee95..3bc2c05d4b 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -117,7 +117,7 @@ You can find example file collections and qMRI maps organized according to BIDS
 
 ## Metadata requirements for qMRI data
 
-The table of required entities for qMRI file collections are provided in the [entity table](../99-appendices/04-entity-table.md).
+The table of required entities for qMRI file collections are provided in the [entity table](./04-entity-table.md).
 However, viability of a qMRI file collection is determined not only by the naming and organization of the input files,
 but also by which metadata fields are provided in accompanying json files.
 
@@ -310,7 +310,7 @@ This approach aims at:
 flavor of qMRI applicaiton for the respective suffix varies across files of a file colleciton
 (which calls for using a linking entity) or fixed. If former is the case, the entity is to be
 added to the files in that file collection. Note that this addition MUST be allowed by the
-priority levels given for that suffix in the [`entity table`](../99-appendices/04-entity-table.md). If latter (`fixed`) is the case,
+priority levels given for that suffix in the [`entity table`](./04-entity-table.md). If latter (`fixed`) is the case,
 filenames will remain the same; however, the optional metadata (third column) may
 define the flavor of the application (fourth column) along with the conditional value of a
 required metadata field (second column).

From 8cd4b12a8a39b0b38a7cca99b9f1c9e8fc96c91b Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 4 Jan 2021 10:55:21 +0100
Subject: [PATCH 45/83] one more link

---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 3bc2c05d4b..8f659aabdd 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -345,7 +345,7 @@ introduce a new suffix:
     (for example, `MP2RAGE`), sequence names are not used as suffixes.
 
 -   File collection suffixes for qMRI applications attain a clear description of the qMRI method that they relate to in the
-    [file collections appendix]((../99-appendices/10-file-collections.md#magnetic-resonance-imaging)).
+    [file collections appendix](./10-file-collections.md#magnetic-resonance-imaging).
 
 -   Hyperlinks to example applications and reference method articles are encouraged whenever possible.
 

From b4f157090bd69841545426a92c2b2ffeabf42c4f Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 11:59:08 -0500
Subject: [PATCH 46/83] Fix typo

---
 .../01-magnetic-resonance-imaging-data.md        | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 2972a73106..649196dc3c 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -148,14 +148,14 @@ non-parametric structural MR images include:
 
 | **Name**                                   | `suffix`         | **Description**                                                                                                                                   |
 | ------------------------------------------ | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- |
-| T1 weighted images                         | T1w              | In arbitrary units (abitrary). The contrast of these images is mainly determined by spatial variations in the longitudinal relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively short repetition and echo times. To achieve this weigthing in gradient-echo images, again, short repetition and echo times are selected; however, at relatively large flip angles. Another common approach to increase T1 weighting in gradient-echo images is to add an inversion preparation block to the beginning of the imaging sequence (for example, `TurboFLASH` or `MP-RAGE`).                           |
-| T2 weighted images                         | T2w              | In arbitrary units (abitrary). The contrast of these images is mainly determined by spatial variations in the (true) transverse relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively long repetition and echo times. Generally, gradient echo sequences are not the most suitable option for achieving T2 weighting, as their contrast natively depends on T2-star rather than on T2.        |
-| Proton density (PD) weighted images        | PDw              | In arbitrary units (abitrary). The contrast of these images is mainly determined by spatial variations in the spin density (1H) of the imaged specimen. In spin-echo sequences this contrast is achieved at short repetition and long echo times. In a gradient-echo acquisition, PD weighting dominates the contrast at long repetition and short echo times, and at small flip angles.|
-| T2star weighted images                     | T2starw          | In arbitrary units (abitrary). The contrast of these images is mainly determined by spatial variations in the (observed) transverse relaxation time of the imaged specimen. In spin-echo sequences, this effect is negated as the excitation is followed by an inversion pulse. The contrast of gradient-echo images natively depends on T2-star effects. However, for T2-star variation to dominate the image contrast, gradient-echo acquisitions are carried out at long repetition and echo times, and at small flip angles.                                                                                                     |
-| Fluid attenuated inversion recovery images | FLAIR            | In arbitrary units (abitrary). Structural images with predominant T2 contribution (a.k.a T2-FLAIR), in which signal from fluids (for example, CSF) is nulled out by adjusting inversion time, coupled with notably long repetition and echo times.                                                  |
-| Inplane T1                                 | inplaneT1        | In arbitrary units (abitrary). T1 weighted structural image matched to a functional (task) image.                                                                                  |
-| Inplane T2                                 | inplaneT2        | In arbitrary units (abitrary). T2 weighted structural image matched to a functional (task) image.                                                                                  |
-| PD and T2 weighted images                  | PDT2             | In arbitrary units (abitrary). PDw and T2w images acquired using a dual echo FSE sequence through view sharing process ([Johnson et al. 1994](https://pubmed.ncbi.nlm.nih.gov/8010268/)).                                      |
+| T1 weighted images                         | T1w              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the longitudinal relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively short repetition and echo times. To achieve this weigthing in gradient-echo images, again, short repetition and echo times are selected; however, at relatively large flip angles. Another common approach to increase T1 weighting in gradient-echo images is to add an inversion preparation block to the beginning of the imaging sequence (for example, `TurboFLASH` or `MP-RAGE`).                           |
+| T2 weighted images                         | T2w              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the (true) transverse relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively long repetition and echo times. Generally, gradient echo sequences are not the most suitable option for achieving T2 weighting, as their contrast natively depends on T2-star rather than on T2.        |
+| Proton density (PD) weighted images        | PDw              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the spin density (1H) of the imaged specimen. In spin-echo sequences this contrast is achieved at short repetition and long echo times. In a gradient-echo acquisition, PD weighting dominates the contrast at long repetition and short echo times, and at small flip angles.|
+| T2star weighted images                     | T2starw          | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the (observed) transverse relaxation time of the imaged specimen. In spin-echo sequences, this effect is negated as the excitation is followed by an inversion pulse. The contrast of gradient-echo images natively depends on T2-star effects. However, for T2-star variation to dominate the image contrast, gradient-echo acquisitions are carried out at long repetition and echo times, and at small flip angles.                                                                                                     |
+| Fluid attenuated inversion recovery images | FLAIR            | In arbitrary units (arbitrary). Structural images with predominant T2 contribution (a.k.a T2-FLAIR), in which signal from fluids (for example, CSF) is nulled out by adjusting inversion time, coupled with notably long repetition and echo times.                                                  |
+| Inplane T1                                 | inplaneT1        | In arbitrary units (arbitrary). T1 weighted structural image matched to a functional (task) image.                                                                                  |
+| Inplane T2                                 | inplaneT2        | In arbitrary units (arbitrary). T2 weighted structural image matched to a functional (task) image.                                                                                  |
+| PD and T2 weighted images                  | PDT2             | In arbitrary units (arbitrary). PDw and T2w images acquired using a dual echo FSE sequence through view sharing process ([Johnson et al. 1994](https://pubmed.ncbi.nlm.nih.gov/8010268/)).                                      |
 
 If the structural images included in the dataset were defaced (to protect
 identity of participants) one MAY provide the binary mask that was used to

From 42cb86b0a5b49a8c4ed2e4a769b41e4766dd1352 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 12:00:50 -0500
Subject: [PATCH 47/83] Fix parantheses

---
 src/99-appendices/11-qmri.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 8f659aabdd..7688917e40 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -299,14 +299,14 @@ This approach aims at:
 -   providing qMRI-focused BIDS applications with a set of meta-data driven rules to infer possible fitting options,
 -   keeping an inheritance track of the qMRI methods described within the specification.
 
-| **File-collection suffix** | **If REQUIRED metadata == Value** | **OPTIONAL metadata [`entity`/`fixed`]**   | **Derived application name (NOT a suffix)** |
+| **File-collection suffix** | **If REQUIRED metadata == Value** | **OPTIONAL metadata (`entity`/`fixed`)**   | **Derived application name (NOT a suffix)** |
 |----------------------------|-----------------------------------|--------------------------------------------|---------------------------------------------|
 | VFA                        | `PulseSequenceType` == `SPGR`     |                                            | DESPOT1                                     |
-| VFA                        | `PulseSequenceType` == `SSFP`     | `SpoilingRFPhaseIncrement` [`fixed`]       | DESPOT2                                     |
-| MP2RAGE                    |                                   | `EchoTime` [`echo`]                        | MP2RAGE-ME                                  |
-| MPM                        |                                   | `EchoTime` [`echo`]                        | MPM-ME                                      |
+| VFA                        | `PulseSequenceType` == `SSFP`     | `SpoilingRFPhaseIncrement` (`fixed`)       | DESPOT2                                     |
+| MP2RAGE                    |                                   | `EchoTime` (`echo`)                        | MP2RAGE-ME                                  |
+| MPM                        |                                   | `EchoTime` (`echo`)                        | MPM-ME                                      |
 
-<sup>*</sup> [`entity`/`fixed`] denotes whether the OPTIONAL metadata that forms a new
+<sup>*</sup> (`entity`/`fixed`) denotes whether the OPTIONAL metadata that forms a new
 flavor of qMRI applicaiton for the respective suffix varies across files of a file colleciton
 (which calls for using a linking entity) or fixed. If former is the case, the entity is to be
 added to the files in that file collection. Note that this addition MUST be allowed by the

From 37db200d1668aaa94f800b31112b33a5f6be19af Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:04:43 -0500
Subject: [PATCH 48/83] Make spoiling-relevant requirements more explicit

---
 .../01-magnetic-resonance-imaging-data.md     | 36 +++++++++----------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 649196dc3c..da438418ba 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -45,24 +45,24 @@ that a given scan was collected with the intended coil elements selected
 
 | **Key name**                | **Requirement level** | **Data type**                          | **Description**                                                                                                                                                                                                                                                           |
 |-----------------------------|-----------------------|----------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| PulseSequenceType           | RECOMMENDED                                    | [string][]                             | A general description of the pulse sequence used for the scan (for example, MPRAGE, Gradient Echo EPI, Spin Echo EPI, Multiband gradient echo EPI).                                                                                                                       |
-| ScanningSequence            | RECOMMENDED                                    | [string][] or [array][] of [strings][] | Description of the type of data acquired. Corresponds to DICOM Tag 0018, 0020 `Scanning Sequence`.                                                                                                                                                                        |
-| SequenceVariant             | RECOMMENDED                                    | [string][] or [array][] of [strings][] | Variant of the ScanningSequence. Corresponds to DICOM Tag 0018, 0021 `Sequence Variant`.                                                                                                                                                                                  |
-| ScanOptions                 | RECOMMENDED                                    | [string][] or [array][] of [strings][] | Parameters of ScanningSequence. Corresponds to DICOM Tag 0018, 0022 `Scan Options`.                                                                                                                                                                                       |
-| SequenceName                | RECOMMENDED                                    | [string][]                             | Manufacturer's designation of the sequence name. Corresponds to DICOM Tag 0018, 0024 `Sequence Name`.                                                                                                                                                                     |
-| PulseSequenceDetails        | RECOMMENDED                                    | [string][]                             | Information beyond pulse sequence type that identifies the specific pulse sequence used (for example, "Standard Siemens Sequence distributed with the VB17 software," "Siemens WIP ### version #.##," or "Sequence written by X using a version compiled on MM/DD/YYYY"). |
-| NonlinearGradientCorrection | RECOMMENDED                                    | [boolean][]                            | Boolean stating if the image saved has been corrected for gradient nonlinearities by the scanner sequence.                                                                                                                                                                |
-| MTState                     | RECOMMENDED                                    | [boolean][]                            | Boolean stating whether the magnetization transfer pulse is applied. Corresponds to DICOM tag (0018, 9020) `Magnetization Transfer`.                                                                                                                                      |
-| MTOffsetFrequency           | RECOMMENDED if the MTstate is `True`.          | [number][]                             | The frequency offset of the magnetization transfer pulse with respect to the central H1 Larmor frequency in Hertz (Hz).                                                                                                                                                   |
-| MTPulseBandwidth            | RECOMMENDED if the MTstate is `True`.          | [number][]                             | The excitation bandwidth of the magnetization transfer pulse in Hertz (Hz).                                                                                                                                                                                               |
-| MTNumberOfPulses            | RECOMMENDED if the MTstate is `True`.          | [number][]                             | The number of magnetization transfer RF pulses applied before the readout.                                                                                                                                                                                         |
-| MTPulseShape                | RECOMMENDED if the MTstate is `True`.          | [string][]                             | Shape of the magnetization transfer RF pulse waveform. Accepted values: `HARD`, `GAUSSIAN`, `GAUSSHANN` (gaussian pulse with Hanning window), `SINC`, `SINCHANN` (sinc pulse with Hanning window), `SINCGAUSS` (sinc pulse with Gaussian window), `FERMI`.                |
-| MTPulseDuration             | RECOMMENDED if the MTstate is `True`.          | [number][]                             | Duration of the magnetization transfer RF pulse in seconds.                                                                                                                                                                                          |
-| SpoilingState               | RECOMMENDED                                    | [boolean][]                            | Boolean stating whether the pulse sequence uses any type of spoiling strategy to suppress residual transverse magnetization.                                                                                                                                           |
-| SpoilingType                | RECOMMENDED if the SpoilingState is `True`.    | [string][]                             | Specifies which spoiling method(s) are used by a spoiled sequence. Accepted values: `RF`, `GRADIENT` or `COMBINED`.                                                                                                                                                  |
-| SpoilingRFPhaseIncrement    | RECOMMENDED if the SpoilingType has `RF`.      | [number][]                             | The amount of incrementation described in degrees, which is applied to the phase of the excitation pulse at each TR period for achieving RF spoiling.                                                                                                                        |
-| SpoilingGradientMoment      | RECOMMENDED if the SpoilingType has `GRADIENT`. | [number][]                            | Zeroth moment of the spoiler gradient lobe in millitesla times second per meter (mT.s/m).                                                                                                                                                                                   |
-| SpoilingGradientDuration    | RECOMMENDED if the SpoilingType has `GRADIENT`. | [number][]                            | The duration of the spoiler gradient lobe in seconds. The duration of a trapezoidal lobe is defined as the summation of ramp-up and plateu times.                                                                                                                                                                                            |
+| PulseSequenceType           | RECOMMENDED                                                 | [string][]                             | A general description of the pulse sequence used for the scan (for example, MPRAGE, Gradient Echo EPI, Spin Echo EPI, Multiband gradient echo EPI).                                                                                                                       |
+| ScanningSequence            | RECOMMENDED                                                 | [string][] or [array][] of [strings][] | Description of the type of data acquired. Corresponds to DICOM Tag 0018, 0020 `Scanning Sequence`.                                                                                                                                                                        |
+| SequenceVariant             | RECOMMENDED                                                 | [string][] or [array][] of [strings][] | Variant of the ScanningSequence. Corresponds to DICOM Tag 0018, 0021 `Sequence Variant`.                                                                                                                                                                                  |
+| ScanOptions                 | RECOMMENDED                                                 | [string][] or [array][] of [strings][] | Parameters of ScanningSequence. Corresponds to DICOM Tag 0018, 0022 `Scan Options`.                                                                                                                                                                                       |
+| SequenceName                | RECOMMENDED                                                 | [string][]                             | Manufacturer's designation of the sequence name. Corresponds to DICOM Tag 0018, 0024 `Sequence Name`.                                                                                                                                                                     |
+| PulseSequenceDetails        | RECOMMENDED                                                 | [string][]                             | Information beyond pulse sequence type that identifies the specific pulse sequence used (for example, "Standard Siemens Sequence distributed with the VB17 software," "Siemens WIP ### version #.##," or "Sequence written by X using a version compiled on MM/DD/YYYY"). |
+| NonlinearGradientCorrection | RECOMMENDED                                                 | [boolean][]                            | Boolean stating if the image saved has been corrected for gradient nonlinearities by the scanner sequence.                                                                                                                                                                |
+| MTState                     | RECOMMENDED                                                 | [boolean][]                            | Boolean stating whether the magnetization transfer pulse is applied. Corresponds to DICOM tag (0018, 9020) `Magnetization Transfer`.                                                                                                                                      |
+| MTOffsetFrequency           | RECOMMENDED if the MTstate is `True`.                       | [number][]                             | The frequency offset of the magnetization transfer pulse with respect to the central H1 Larmor frequency in Hertz (Hz).                                                                                                                                                   |
+| MTPulseBandwidth            | RECOMMENDED if the MTstate is `True`.                       | [number][]                             | The excitation bandwidth of the magnetization transfer pulse in Hertz (Hz).                                                                                                                                                                                               |
+| MTNumberOfPulses            | RECOMMENDED if the MTstate is `True`.                       | [number][]                             | The number of magnetization transfer RF pulses applied before the readout.                                                                                                                                                                                         |
+| MTPulseShape                | RECOMMENDED if the MTstate is `True`.                       | [string][]                             | Shape of the magnetization transfer RF pulse waveform. Accepted values: `HARD`, `GAUSSIAN`, `GAUSSHANN` (gaussian pulse with Hanning window), `SINC`, `SINCHANN` (sinc pulse with Hanning window), `SINCGAUSS` (sinc pulse with Gaussian window), `FERMI`.                |
+| MTPulseDuration             | RECOMMENDED if the MTstate is `True`.                       | [number][]                             | Duration of the magnetization transfer RF pulse in seconds.                                                                                                                                                                                          |
+| SpoilingState               | RECOMMENDED                                                 | [boolean][]                            | Boolean stating whether the pulse sequence uses any type of spoiling strategy to suppress residual transverse magnetization.                                                                                                                                           |
+| SpoilingType                | RECOMMENDED if the SpoilingState is `True`.                 | [string][]                             | Specifies which spoiling method(s) are used by a spoiled sequence. Accepted values: `RF`, `GRADIENT` or `COMBINED`.                                                                                                                                                  |
+| SpoilingRFPhaseIncrement    | RECOMMENDED if the SpoilingType is `RF` or `COMBINED`.      | [number][]                             | The amount of incrementation described in degrees, which is applied to the phase of the excitation pulse at each TR period for achieving RF spoiling.                                                                                                                        |
+| SpoilingGradientMoment      | RECOMMENDED if the SpoilingType is `GRADIENT` or `COMBINED`. | [number][]                            | Zeroth moment of the spoiler gradient lobe in millitesla times second per meter (mT.s/m).                                                                                                                                                                                   |
+| SpoilingGradientDuration    | RECOMMENDED if the SpoilingType is `GRADIENT` or `COMBINED`. | [number][]                            | The duration of the spoiler gradient lobe in seconds. The duration of a trapezoidal lobe is defined as the summation of ramp-up and plateu times.                                                                                                                                                                                            |
 
 ### In-Plane Spatial Encoding
 | **Key name**                   | **Requirement level** | **Data type** | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |

From 2fd6edc6e57ea5e8717af5094cf67c146be9bc89 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:05:56 -0500
Subject: [PATCH 49/83] Wording suggestion

---
 .../01-magnetic-resonance-imaging-data.md                       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index da438418ba..fec37aae1d 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -67,7 +67,7 @@ that a given scan was collected with the intended coil elements selected
 ### In-Plane Spatial Encoding
 | **Key name**                   | **Requirement level** | **Data type** | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
 |--------------------------------|-----------------------|---------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| NumberShots                    | RECOMMENDED           | [number][] or [array][] of [numbers]    | The number of RF excitations needed to reconstruct a slice or volume (may be referred as partition). Please mind that this is not the same as Echo Train Length which denotes the number of k-space lines collected after excitation in a multi-echo readout.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
+| NumberShots                    | RECOMMENDED           | [number][] or [array][] of [numbers]    | The number of RF excitations needed to reconstruct a slice or volume (may be referred to as partition). Please mind that this is not the same as Echo Train Length which denotes the number of k-space lines collected after excitation in a multi-echo readout.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
 | ParallelReductionFactorInPlane | RECOMMENDED           | [number][]    | The parallel imaging (for instance, GRAPPA) factor. Use the denominator of the fraction of k-space encoded for each slice. For example, 2 means half of k-space is encoded. Corresponds to DICOM Tag 0018, 9069 `Parallel Reduction Factor In-plane`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
 | ParallelAcquisitionTechnique   | RECOMMENDED           | [string][]    | The type of parallel imaging used (for example GRAPPA, SENSE). Corresponds to DICOM Tag 0018, 9078 `Parallel Acquisition Technique`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
 | PartialFourier                 | RECOMMENDED           | [number][]    | The fraction of partial Fourier information collected. Corresponds to DICOM Tag 0018, 9081 `Partial Fourier`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |

From a708ab7664deba7714fe476f182c2a3d1e986d30 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:09:17 -0500
Subject: [PATCH 50/83] Add unit for MixingTime

---
 .../01-magnetic-resonance-imaging-data.md                       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index fec37aae1d..c0f589e342 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -75,7 +75,7 @@ that a given scan was collected with the intended coil elements selected
 | PhaseEncodingDirection         | RECOMMENDED           | [string][]    | Possible values: `i`, `j`, `k`, `i-`, `j-`, `k-`. The letters `i`, `j`, `k` correspond to the first, second and third axis of the data in the NIFTI file. The polarity of the phase encoding is assumed to go from zero index to maximum index unless `-` sign is present (then the order is reversed - starting from the highest index instead of zero). `PhaseEncodingDirection` is defined as the direction along which phase is was modulated which may result in visible distortions. Note that this is not the same as the DICOM term `InPlanePhaseEncodingDirection` which can have `ROW` or `COL` values. This parameter is REQUIRED if corresponding fieldmap data is present or when using multiple runs with different phase encoding directions (which can be later used for field inhomogeneity correction). |
 | EffectiveEchoSpacing           | RECOMMENDED           | [number][]    | The "effective" sampling interval, specified in seconds, between lines in the phase-encoding direction, defined based on the size of the reconstructed image in the phase direction. It is frequently, but incorrectly, referred to as "dwell time" (see `DwellTime` parameter below for actual dwell time). It is required for unwarping distortions using field maps. Note that beyond just in-plane acceleration, a variety of other manipulations to the phase encoding need to be accounted for properly, including partial fourier, phase oversampling, phase resolution, phase field-of-view and interpolation.<sup>2</sup> This parameter is REQUIRED if corresponding fieldmap data is present.                                                                                                                  |
 | TotalReadoutTime               | RECOMMENDED           | [number][]    | This is actually the "effective" total readout time , defined as the readout duration, specified in seconds, that would have generated data with the given level of distortion. It is NOT the actual, physical duration of the readout train. If `EffectiveEchoSpacing` has been properly computed, it is just `EffectiveEchoSpacing * (ReconMatrixPE - 1)`.<sup>3</sup> . This parameter is REQUIRED if corresponding "field/distortion" maps acquired with opposing phase encoding directions are present (see 8.9.4).                                                                                                                                                                                                                                                                                                  |
-| MixingTime                     | RECOMMENDED           | [number][]    | In the context of a stimulated- and spin-echo 3D EPI sequence for B1+ mapping, corresponds to the interval between spin- and stimulated-echo pulses. In the context of a diffusion-weighted double spin-echo sequence, corresponds to the interval between two successive diffusion sensitizing gradients.                                                                                                                                                                                                                                                                                            |
+| MixingTime                     | RECOMMENDED           | [number][]    | In the context of a stimulated- and spin-echo 3D EPI sequence for B1+ mapping, corresponds to the interval between spin- and stimulated-echo pulses. In the context of a diffusion-weighted double spin-echo sequence, corresponds to the interval between two successive diffusion sensitizing gradients, specified in seconds.                                                                                                                                                                                                                                                                                            |
 
 <sup>2</sup>Conveniently, for Siemens data, this value is easily obtained as
 `1 / (BWPPPE * ReconMatrixPE)`, where BWPPPE is the

From dbe5bf429ec5942ac6cc53802cfae53e92739a71 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:10:07 -0500
Subject: [PATCH 51/83] Fix typo

---
 .../01-magnetic-resonance-imaging-data.md                       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index c0f589e342..437085e38b 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -148,7 +148,7 @@ non-parametric structural MR images include:
 
 | **Name**                                   | `suffix`         | **Description**                                                                                                                                   |
 | ------------------------------------------ | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- |
-| T1 weighted images                         | T1w              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the longitudinal relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively short repetition and echo times. To achieve this weigthing in gradient-echo images, again, short repetition and echo times are selected; however, at relatively large flip angles. Another common approach to increase T1 weighting in gradient-echo images is to add an inversion preparation block to the beginning of the imaging sequence (for example, `TurboFLASH` or `MP-RAGE`).                           |
+| T1 weighted images                         | T1w              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the longitudinal relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively short repetition and echo times. To achieve this weighting in gradient-echo images, again, short repetition and echo times are selected; however, at relatively large flip angles. Another common approach to increase T1 weighting in gradient-echo images is to add an inversion preparation block to the beginning of the imaging sequence (for example, `TurboFLASH` or `MP-RAGE`).                           |
 | T2 weighted images                         | T2w              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the (true) transverse relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively long repetition and echo times. Generally, gradient echo sequences are not the most suitable option for achieving T2 weighting, as their contrast natively depends on T2-star rather than on T2.        |
 | Proton density (PD) weighted images        | PDw              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the spin density (1H) of the imaged specimen. In spin-echo sequences this contrast is achieved at short repetition and long echo times. In a gradient-echo acquisition, PD weighting dominates the contrast at long repetition and short echo times, and at small flip angles.|
 | T2star weighted images                     | T2starw          | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the (observed) transverse relaxation time of the imaged specimen. In spin-echo sequences, this effect is negated as the excitation is followed by an inversion pulse. The contrast of gradient-echo images natively depends on T2-star effects. However, for T2-star variation to dominate the image contrast, gradient-echo acquisitions are carried out at long repetition and echo times, and at small flip angles.                                                                                                     |

From 7fa7e070c1f5867d8a4c1e814d97b3b6e2dea69b Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:15:26 -0500
Subject: [PATCH 52/83] Define R1,R2,R2star and re-arrange rows

---
 .../01-magnetic-resonance-imaging-data.md                   | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 437085e38b..191713e05b 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -244,11 +244,11 @@ constitute parametric maps. Currently supported parametric maps include:
 | **Name**                                     | `suffix`  | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
 |----------------------------------------------|-----------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
 | Longitudinal relaxation time map             | T1map     | In seconds (s). T1 maps are REQUIRED to use this suffix regardless of the method used to generate them. See [this interactive book on T1 mapping](https://qmrlab.org/t1_book/intro) for further reading on T1-mapping.                                                                                                                                                                                                                                                                                            |
+| Longitudinal relaxation rate map             | R1map     | In seconds<sup>-1</sup> (1/s). R1 maps (R1 = 1/T1) are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                            |
 | True transverse relaxation time map          | T2map     | In seconds (s). T2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                                           |
+| True transverse relaxation rate map          | R2map     | In seconds<sup>-1</sup> (1/s). R2 maps (R2 = 1/T2) are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                            |
 | Observed transverse relaxation time map      | T2starmap | In seconds (s). T2-star maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                                      |
-| Longitudinal relaxation rate map             | R1map     | In seconds<sup>-1</sup> (1/s). R1 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                            |
-| True transverse relaxation rate map          | R2map     | In seconds<sup>-1</sup> (1/s). R2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                            |
-| Observed transverse relaxation rate map      | R2starmap | In seconds<sup>-1</sup> (1/s). R2-star maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                       |
+| Observed transverse relaxation rate map      | R2starmap | In seconds<sup>-1</sup> (1/s). R2-star maps (R2star = 1/T2star) are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                       |
 | Proton density map                           | PDmap     | In arbitrary units (arbitrary). PD maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                           |
 | Magnetization transfer ratio map             | MTRmap    | In arbitrary units (arbitrary). MTR maps are REQUIRED to use this suffix regardless of the method used to generate them. MTRmap intensity values are RECOMMENDED to be represented in percentage in the range of 0-100%.                                                                                                                                                                                                                                                                                                                                                                                                       |
 | Magnetization transfer saturation map        | MTsat     | In arbitrary units (arbitrary). MTsat maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                        |

From 8f3a13e23ce318283a51a565dc7ae5ab4ebd6852 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:16:21 -0500
Subject: [PATCH 53/83] Fix double quotes

---
 src/99-appendices/11-qmri.md | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 7688917e40..2c2d514577 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -264,14 +264,14 @@ sub-01_T1map.json:
 
 <<Parameters that are constant across files in the (parent) file collection>>
 
-"MagneticFieldStrength”: "3”,
-"Manufacturer”: "Siemens”,
-"ManufacturerModelName”: "TrioTim”,
-"InstitutionName”: "xxx”,
-"PulseSequenceType”: "SPGR”,
-"PulseSequenceDetails”: "Information beyond the sequence type that identifies
+"MagneticFieldStrength": "3",
+"Manufacturer": "Siemens",
+"ManufacturerModelName": "TrioTim",
+"InstitutionName": "xxx",
+"PulseSequenceType": "SPGR",
+"PulseSequenceDetails": "Information beyond the sequence type that identifies
  specific pulse sequence used (VB version, if not standard, Siemens WIP XXX
- ersion ### sequence written by xx using a version compiled on mm/dd/yyyy/)”,
+ ersion ### sequence written by xx using a version compiled on mm/dd/yyyy/)",
 "RepetitionTimeExcitation": "35",
 "EchoTime": "2.86",
 "SliceThickness": "5",

From 35f63755f1ffb4c5a93c48cef2f12dbbd96e8b7e Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:16:59 -0500
Subject: [PATCH 54/83] Fix typo

---
 src/99-appendices/11-qmri.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 2c2d514577..09cbbb2918 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -285,7 +285,7 @@ sub-01_T1map.json:
 
 ## Deriving the intended qMRI application from an ambiguous file collection
 
-Certain file colleciton suffixes may refer to a generic data collection regime such as variable flip angle (VFA),
+Certain file collection suffixes may refer to a generic data collection regime such as variable flip angle (VFA),
 rather than a more specific acquisition, for example, magnetization prepared two gradient echoes (MP2RAGE).
 Such generic acquisitions can serve as a basis to derive various qMRI applications by changes to the acquisition sequence
 (for example, readout) type or by varying additional scan parameters.
@@ -307,7 +307,7 @@ This approach aims at:
 | MPM                        |                                   | `EchoTime` (`echo`)                        | MPM-ME                                      |
 
 <sup>*</sup> (`entity`/`fixed`) denotes whether the OPTIONAL metadata that forms a new
-flavor of qMRI applicaiton for the respective suffix varies across files of a file colleciton
+flavor of qMRI applicaiton for the respective suffix varies across files of a file collection
 (which calls for using a linking entity) or fixed. If former is the case, the entity is to be
 added to the files in that file collection. Note that this addition MUST be allowed by the
 priority levels given for that suffix in the [`entity table`](./04-entity-table.md). If latter (`fixed`) is the case,

From a683f40d51c9feaa8f189bfaeaa0e6d77531026b Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:18:04 -0500
Subject: [PATCH 55/83] Wording suggestion

---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 09cbbb2918..365b126613 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -335,7 +335,7 @@ column of [the priority levels table](#Method-specific-priority-levels-for-qMRI-
 
 ## Introducing a new qMRI file collection
 
-If a qMRI application can not be interpreted as subset of an already existing suffix
+If a qMRI application cannot be interpreted as a subtype of an already existing suffix
 of a qMRI-related file collection, we RECOMMEND adhering to the following principles to
 introduce a new suffix:
 

From 10833a8e6c4d3863eebc4325c0d793d5dff71203 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:18:39 -0500
Subject: [PATCH 56/83] Rm verbosity

---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 365b126613..fecdae9bea 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -388,7 +388,7 @@ If an additional `UNIT1` image is calculated offline, then the output is to be s
 
 Note that type of `NumberShots` field can be either a `number` or an `array of numbers`.
 
--   If a single `number` is to be provided, this should correspond to the number of `SlicesPerSlab` or `ReconMatrixPE`.
+-   If a single `number` is provided, this should correspond to the number of `SlicesPerSlab` or `ReconMatrixPE`.
     However, in this case, `SlicePartialFourier` or `PartialFourierPE` fraction is needed
     to calculate the number of partitions `before` and `after` of the k-space center to calculate a T1 map.
 

From 3f33e1d7208f50c4caf53c24794dcfd9552894be Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:19:11 -0500
Subject: [PATCH 57/83] Wording fix

---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index fecdae9bea..e32c678f65 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -410,7 +410,7 @@ See this [reference](https://github.com/JosePMarques/MP2RAGE-related-scripts/blo
 
 ##### Other metadata fields
 
-The value of the `RepetitionTimeExcitation` is not commonly found in the DICOM files.
+The value of the `RepetitionTimeExcitation` field is not commonly found in the DICOM files.
 When accessible, the value of `EchoSpacing` corresponds to this metadata.
 When not accessible, `2 X EchoTime` can be used as a surrogate.
 

From 09d8d1a4a7d45d709a3f3f26c73bf0d10a236bc5 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:45:29 -0500
Subject: [PATCH 58/83] Number of shots array/number explanation

---
 .../01-magnetic-resonance-imaging-data.md                       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 191713e05b..d6a5b57be4 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -67,7 +67,7 @@ that a given scan was collected with the intended coil elements selected
 ### In-Plane Spatial Encoding
 | **Key name**                   | **Requirement level** | **Data type** | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
 |--------------------------------|-----------------------|---------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| NumberShots                    | RECOMMENDED           | [number][] or [array][] of [numbers]    | The number of RF excitations needed to reconstruct a slice or volume (may be referred to as partition). Please mind that this is not the same as Echo Train Length which denotes the number of k-space lines collected after excitation in a multi-echo readout.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
+| NumberShots                    | RECOMMENDED           | [number][] or [array][] of [numbers]    | The number of RF excitations needed to reconstruct a slice or volume (may be referred to as partition). Please mind that this is not the same as Echo Train Length which denotes the number of k-space lines collected after excitation in a multi-echo readout. The data type array is applicable for specifying this parameter before and after the k-space center is sampled. Plase see [this note](../99-appendices/11-qmri.md#NumberShots-metadata-field) for corresponding calculations.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
 | ParallelReductionFactorInPlane | RECOMMENDED           | [number][]    | The parallel imaging (for instance, GRAPPA) factor. Use the denominator of the fraction of k-space encoded for each slice. For example, 2 means half of k-space is encoded. Corresponds to DICOM Tag 0018, 9069 `Parallel Reduction Factor In-plane`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
 | ParallelAcquisitionTechnique   | RECOMMENDED           | [string][]    | The type of parallel imaging used (for example GRAPPA, SENSE). Corresponds to DICOM Tag 0018, 9078 `Parallel Acquisition Technique`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
 | PartialFourier                 | RECOMMENDED           | [number][]    | The fraction of partial Fourier information collected. Corresponds to DICOM Tag 0018, 9081 `Partial Fourier`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |

From c781797636f71315af90222c312c2de2c77fce65 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:47:19 -0500
Subject: [PATCH 59/83] Update
 src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 .../01-magnetic-resonance-imaging-data.md                    | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index d6a5b57be4..3dc76a6444 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -276,8 +276,9 @@ them, visit the [qMRI appendix](../99-appendices/11-qmri.md).
 ### Deprecated suffixes
 
 Some suffixes that were available in versions of the specification prior to
-1.5.0. have been deprecated. These suffixes are ambiguous and have been superseded
-by more precise conventions. Therefore, they are not recommended for use in new datasets.
+1.5.0 have been deprecated.
+These suffixes are ambiguous and have been superseded by more precise conventions.
+Therefore, they are not recommended for use in new datasets.
 They are, however, still valid suffixes, to maintain backwards compatibility.
 
 The following suffixes are valid, but SHOULD NOT be used for new BIDS compatible

From 69cb435cabd4bb2119d6526f1f1700bad4fe30ca Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:47:30 -0500
Subject: [PATCH 60/83] Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index e32c678f65..a2a37046d5 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -2,7 +2,7 @@
 
 Quantitative MRI (qMRI) is a collection of methods aiming at generating parametric maps
 that can characterize underlying tissue properties.
-Unlike that of conventional MR images (for example, `T1w`, `T2w`),
+Unlike those of conventional MR images (for example, `T1w` or `T2w`),
 intensity values of quantitative maps are not represented in an arbitrary grayscale range.
 Instead, these maps are represented either in absolute physical units
 (for example, `seconds` for `T1map`),

From fcea48e5b452fc0630f1545d3cf2086ec847733d Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:47:43 -0500
Subject: [PATCH 61/83] Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index a2a37046d5..8879a0f5c0 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -37,7 +37,7 @@ There are two main ways to obtain a quantitative map:
 
 The common concept of [entity-linked file collections](../02-common-principles.md#entity-linked-file-collections) enables the description of a qMRI
 application by creating logical groups of input files through `suffix` and certain entities
-representing acquisition parameters (`echo`, `flip`,`inv`, `mt`) or file parts (`part`).
+representing acquisition parameters (`echo`, `flip`, `inv`, `mt`) or file parts (`part`).
 
 If a qMRI file collection is intended for creating structural quantitative maps (for example, `T1map`),
 files belonging to that collection are stored in the `anat` subfolder.

From e13643d0623dde135144ab70f6ede2432ba64e76 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:48:03 -0500
Subject: [PATCH 62/83] Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/99-appendices/11-qmri.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 8879a0f5c0..c9189a33af 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -419,7 +419,8 @@ Further information about other `MP2RAGE` qMRI protocol fields can be found [her
 #### `TB1SRGE` specific notes
 
 Calculation of `before` and `after` entries for `NumberShots` metadata field of `TB1SRGE` is more involved than that of `MP2RAGE`.
-The formula can be found [here](https://github.com/JosePMarques/MP2RAGE-related-scripts/blob/a405df30ac2c617d29d8b1b16025aaa911e86370/DemoForR1Correction.m#L17),
+The formula can be found in a
+[reference implementation](https://github.com/JosePMarques/MP2RAGE-related-scripts/blob/a405df30ac2c617d29d8b1b16025aaa911e86370/DemoForR1Correction.m#L17),
 which requires information about `BaseResolution` (that is, image matrix size in PE direction),
 partial Fourier fraction in the PE direction, number of reference lines for parallel imaging acceleration,
 and the parallel imaging acceleration factor in PE direction.

From 87e456b5420b02d2340850c924d2a6f3815990b0 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:48:22 -0500
Subject: [PATCH 63/83] Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/99-appendices/11-qmri.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index c9189a33af..d5e1c81a9b 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -414,7 +414,8 @@ The value of the `RepetitionTimeExcitation` field is not commonly found in the D
 When accessible, the value of `EchoSpacing` corresponds to this metadata.
 When not accessible, `2 X EchoTime` can be used as a surrogate.
 
-Further information about other `MP2RAGE` qMRI protocol fields can be found [here](https://qmrlab.readthedocs.io/en/master/protocols.html#mp2rage).
+Further information about other `MP2RAGE` qMRI protocol fields can be found in the
+[qMRLab documentation](https://qmrlab.readthedocs.io/en/master/protocols.html#mp2rage).
 
 #### `TB1SRGE` specific notes
 

From 260e00292b71d890689e74c6664f9f899b1e793e Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:48:32 -0500
Subject: [PATCH 64/83] Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index d5e1c81a9b..7d53310ab6 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -406,7 +406,7 @@ before = SlicesPerSlab*(SlicePartialFourier - 0.5)
 after  = SlicesPerSlab/2
 ```
 
-See this [reference](https://github.com/JosePMarques/MP2RAGE-related-scripts/blob/a405df30ac2c617d29d8b1b16025aaa911e86370/func/bids_T1B1correct.m#L16).
+See this [reference implementation](https://github.com/JosePMarques/MP2RAGE-related-scripts/blob/a405df30ac2c617d29d8b1b16025aaa911e86370/func/bids_T1B1correct.m#L16).
 
 ##### Other metadata fields
 

From 42848649749b9c463076f41939a1e666a4c4962c Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:48:50 -0500
Subject: [PATCH 65/83] Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 7d53310ab6..a00ae2adcc 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -386,7 +386,7 @@ If an additional `UNIT1` image is calculated offline, then the output is to be s
 
 ##### `NumberShots` metadata field
 
-Note that type of `NumberShots` field can be either a `number` or an `array of numbers`.
+Note that the type of `NumberShots` field can be either a `number` or an `array of numbers`.
 
 -   If a single `number` is provided, this should correspond to the number of `SlicesPerSlab` or `ReconMatrixPE`.
     However, in this case, `SlicePartialFourier` or `PartialFourierPE` fraction is needed

From a9b2801af08b93720bb31368243d03f35f7b016f Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:49:37 -0500
Subject: [PATCH 66/83] Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/99-appendices/11-qmri.md | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index a00ae2adcc..88a144a6ca 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -428,14 +428,12 @@ and the parallel imaging acceleration factor in PE direction.
 
 ### Radiofrequency (RF) field mapping
 
-General notes:
-
--   Some RF file collections call for the use of special notations that cannot be resolved by
-    by entities that can generalize to other applications.
-    Instead of introducing an entity that is exclusive to a single application,
-    method developers who commonly use these file collections for the `MPM` application reached
-    the consensus on the use of `acq` entity to distinguish individual files.
-    These suffixes include: `TB1AFI`, `TB1TFL`, `TB1RMF`, and `RB1COR`.
+Some RF file collections call for the use of special notations that cannot be resolved by
+by entities that can generalize to other applications.
+Instead of introducing an entity that is exclusive to a single application,
+method developers who commonly use these file collections for the `MPM` application reached
+the consensus on the use of `acq` entity to distinguish individual files.
+These suffixes include: `TB1AFI`, `TB1TFL`, `TB1RMF`, and `RB1COR`.
 
 #### `TB1EPI` specific notes
 

From 5326eaadd8126af4ce00dfb3b330ae235877a7e8 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:50:02 -0500
Subject: [PATCH 67/83] Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 88a144a6ca..532993420a 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -145,7 +145,7 @@ Explanation of the table:
 
 -   Note that some of the metadata fields may be constant across different files in a file collection,
     yet still required as an input (for example, `NumberShots` in `MP2AGE`).
-    Such metadata fields MUST be provided in the accompanying json files.
+    Such metadata fields MUST be provided in the accompanying JSON files.
 
 -   The metadata fields listed in the OPTIONAL column can be used to form different flavors of an existing file collection suffix,
     dispensing with the need for introducing a new suffix.

From 70244b1d895830f74c99f5626eb1ce7586d4a47e Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:50:29 -0500
Subject: [PATCH 68/83] Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 532993420a..7cf85011e9 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -306,7 +306,7 @@ This approach aims at:
 | MP2RAGE                    |                                   | `EchoTime` (`echo`)                        | MP2RAGE-ME                                  |
 | MPM                        |                                   | `EchoTime` (`echo`)                        | MPM-ME                                      |
 
-<sup>*</sup> (`entity`/`fixed`) denotes whether the OPTIONAL metadata that forms a new
+In this table, (`entity`/`fixed`) denotes whether the OPTIONAL metadata that forms a new
 flavor of qMRI applicaiton for the respective suffix varies across files of a file collection
 (which calls for using a linking entity) or fixed. If former is the case, the entity is to be
 added to the files in that file collection. Note that this addition MUST be allowed by the

From 0a85224c8efb33a31d5a0e7d44b736d551678d57 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:52:05 -0500
Subject: [PATCH 69/83] Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 7cf85011e9..b6dc672aaa 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -375,7 +375,7 @@ Although the `UNIT1` image is provided as an output by the acquisition sequence,
 as an input to offline calculation of a `T1map` using a dictionary lookup approach. However,
 `complex` data is needed for an accurate calculation of the `UNIT1` image, which is not commonly
 provided by the stock sequence. Instead, the `magnitude` and `phase` images are exported. Please
-see the relevant discussion [here](https://github.com/qMRLab/qMRLab/issues/255).
+see the relevant discussion at [qMRLab issue #255](https://github.com/qMRLab/qMRLab/issues/255).
 
 Therefore, the `UNIT1` image provided by the scanner is RECOMMENDED to be stored under the `anat`
 raw dataset directory along with the `MP2RAGE` file collection and to be used as the primary input

From c4396f01594dfc0ada96bb61bba5325800ba9d35 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 14:52:38 -0500
Subject: [PATCH 70/83] Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index b6dc672aaa..30bb60b798 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -320,7 +320,7 @@ listed for the respective file collection suffix are provided for the data. In a
 conditional rules based on the value of a given required metada field can be set
 for the description of a derived qMRI application. Note that the value of this
 required metadata is fixed across constituent images of a file collection and defined
-in [this section](#Method-specific-priority-levels-for-qMRI-file-collections).
+in [Method-specific priority levels for qMRI file collections](#Method-specific-priority-levels-for-qMRI-file-collections).
 
 For example, if the optional metadata field of `PulseSequenceType` is SPGR
 for a collection of anatomical images listed by the `VFA` suffix, the data

From e6410edccc994df8a8c4e1c64bdb332571e974be Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Mon, 4 Jan 2021 16:55:04 -0500
Subject: [PATCH 71/83] Update
 src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 .../01-magnetic-resonance-imaging-data.md                       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 3dc76a6444..02b07ce073 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -67,7 +67,7 @@ that a given scan was collected with the intended coil elements selected
 ### In-Plane Spatial Encoding
 | **Key name**                   | **Requirement level** | **Data type** | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
 |--------------------------------|-----------------------|---------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| NumberShots                    | RECOMMENDED           | [number][] or [array][] of [numbers]    | The number of RF excitations needed to reconstruct a slice or volume (may be referred to as partition). Please mind that this is not the same as Echo Train Length which denotes the number of k-space lines collected after excitation in a multi-echo readout. The data type array is applicable for specifying this parameter before and after the k-space center is sampled. Plase see [this note](../99-appendices/11-qmri.md#NumberShots-metadata-field) for corresponding calculations.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
+| NumberShots                    | RECOMMENDED           | [number][] or [array][] of [numbers]    | The number of RF excitations needed to reconstruct a slice or volume (may be referred to as partition). Please mind that this is not the same as Echo Train Length which denotes the number of k-space lines collected after excitation in a multi-echo readout. The data type array is applicable for specifying this parameter before and after the k-space center is sampled. Plase see [`NumberShots` metadata field](../99-appendices/11-qmri.md#NumberShots-metadata-field) in the qMRI appendix for corresponding calculations.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
 | ParallelReductionFactorInPlane | RECOMMENDED           | [number][]    | The parallel imaging (for instance, GRAPPA) factor. Use the denominator of the fraction of k-space encoded for each slice. For example, 2 means half of k-space is encoded. Corresponds to DICOM Tag 0018, 9069 `Parallel Reduction Factor In-plane`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
 | ParallelAcquisitionTechnique   | RECOMMENDED           | [string][]    | The type of parallel imaging used (for example GRAPPA, SENSE). Corresponds to DICOM Tag 0018, 9078 `Parallel Acquisition Technique`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
 | PartialFourier                 | RECOMMENDED           | [number][]    | The fraction of partial Fourier information collected. Corresponds to DICOM Tag 0018, 9081 `Partial Fourier`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |

From 8f554cfc6a10a6f36b25c7a15bdae63761e1cf65 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Wed, 6 Jan 2021 16:14:08 +0100
Subject: [PATCH 72/83] fix links by converting to lowercase

---
 .../01-magnetic-resonance-imaging-data.md            |  2 +-
 src/99-appendices/11-qmri.md                         | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 02b07ce073..b05bd21a31 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -67,7 +67,7 @@ that a given scan was collected with the intended coil elements selected
 ### In-Plane Spatial Encoding
 | **Key name**                   | **Requirement level** | **Data type** | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
 |--------------------------------|-----------------------|---------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| NumberShots                    | RECOMMENDED           | [number][] or [array][] of [numbers]    | The number of RF excitations needed to reconstruct a slice or volume (may be referred to as partition). Please mind that this is not the same as Echo Train Length which denotes the number of k-space lines collected after excitation in a multi-echo readout. The data type array is applicable for specifying this parameter before and after the k-space center is sampled. Plase see [`NumberShots` metadata field](../99-appendices/11-qmri.md#NumberShots-metadata-field) in the qMRI appendix for corresponding calculations.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
+| NumberShots                    | RECOMMENDED           | [number][] or [array][] of [numbers]    | The number of RF excitations needed to reconstruct a slice or volume (may be referred to as partition). Please mind that this is not the same as Echo Train Length which denotes the number of k-space lines collected after excitation in a multi-echo readout. The data type array is applicable for specifying this parameter before and after the k-space center is sampled. Plase see [`NumberShots` metadata field](../99-appendices/11-qmri.md#numbershots-metadata-field) in the qMRI appendix for corresponding calculations.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
 | ParallelReductionFactorInPlane | RECOMMENDED           | [number][]    | The parallel imaging (for instance, GRAPPA) factor. Use the denominator of the fraction of k-space encoded for each slice. For example, 2 means half of k-space is encoded. Corresponds to DICOM Tag 0018, 9069 `Parallel Reduction Factor In-plane`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
 | ParallelAcquisitionTechnique   | RECOMMENDED           | [string][]    | The type of parallel imaging used (for example GRAPPA, SENSE). Corresponds to DICOM Tag 0018, 9078 `Parallel Acquisition Technique`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
 | PartialFourier                 | RECOMMENDED           | [number][]    | The fraction of partial Fourier information collected. Corresponds to DICOM Tag 0018, 9081 `Partial Fourier`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 30bb60b798..bc6724151f 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -149,7 +149,7 @@ Explanation of the table:
 
 -   The metadata fields listed in the OPTIONAL column can be used to form different flavors of an existing file collection suffix,
     dispensing with the need for introducing a new suffix.
-    See [deriving the intended qMRI application from an ambiguos file collection](#Deriving-the-intended-qMRI-application-from-an-ambiguous-file-collection)
+    See [deriving the intended qMRI application from an ambiguous file collection](#deriving-the-intended-qmri-application-from-an-ambiguous-file-collection)
     for details.
 
 #### Field maps
@@ -320,7 +320,7 @@ listed for the respective file collection suffix are provided for the data. In a
 conditional rules based on the value of a given required metada field can be set
 for the description of a derived qMRI application. Note that the value of this
 required metadata is fixed across constituent images of a file collection and defined
-in [Method-specific priority levels for qMRI file collections](#Method-specific-priority-levels-for-qMRI-file-collections).
+in [Method-specific priority levels for qMRI file collections](#method-specific-priority-levels-for-qmri-file-collections).
 
 For example, if the optional metadata field of `PulseSequenceType` is SPGR
 for a collection of anatomical images listed by the `VFA` suffix, the data
@@ -330,8 +330,8 @@ provided as a metadata field, then the dataset becomes eligible for `DESPOT2`
 T2 fitting application.
 
 Please note that optional metadata fields listed in the [deriving the intended qMRI
-application from an ambiguous file collection table](#Deriving-the-intended-qMRI-application-from-an-ambiguous-file-collection) are included in the optional (third)
-column of [the priority levels table](#Method-specific-priority-levels-for-qMRI-file-collections) for the consistency of this appendix.
+application from an ambiguous file collection table](#deriving-the-intended-qmri-application-from-an-ambiguous-file-collection) are included in the optional (third)
+column of [the priority levels table](#method-specific-priority-levels-for-qmri-file-collections) for the consistency of this appendix.
 
 ## Introducing a new qMRI file collection
 
@@ -351,9 +351,9 @@ introduce a new suffix:
 
 -   If it is possible to derive a qMRI application from an already existing file collection suffix
     by defining a set of logical conditions over the metadata fields, the tables of the
-    [deriving the intended qMRI application from an ambiguous file collection](#Deriving-the-intended-qMRI-application-from-an-ambiguous-file-collection)
+    [deriving the intended qMRI application from an ambiguous file collection](#deriving-the-intended-qmri-application-from-an-ambiguous-file-collection)
     and the
-    [anatomy data priority levels](#Anatomy-imaging-data)
+    [anatomy data priority levels](#anatomy-imaging-data)
     sections are extended instead of introducing a new suffix.
 
 ## Application-specific notes for qMRI file collections

From 20e390cbde994a205130b2d708f3fcd98972c54a Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 6 Jan 2021 11:36:51 -0500
Subject: [PATCH 73/83] STY: Align table fences

---
 .../01-magnetic-resonance-imaging-data.md     | 100 +++++++++---------
 1 file changed, 50 insertions(+), 50 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index b05bd21a31..4adaf42cd9 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -43,39 +43,39 @@ that a given scan was collected with the intended coil elements selected
 
 ### Sequence Specifics
 
-| **Key name**                | **Requirement level** | **Data type**                          | **Description**                                                                                                                                                                                                                                                           |
-|-----------------------------|-----------------------|----------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| PulseSequenceType           | RECOMMENDED                                                 | [string][]                             | A general description of the pulse sequence used for the scan (for example, MPRAGE, Gradient Echo EPI, Spin Echo EPI, Multiband gradient echo EPI).                                                                                                                       |
-| ScanningSequence            | RECOMMENDED                                                 | [string][] or [array][] of [strings][] | Description of the type of data acquired. Corresponds to DICOM Tag 0018, 0020 `Scanning Sequence`.                                                                                                                                                                        |
-| SequenceVariant             | RECOMMENDED                                                 | [string][] or [array][] of [strings][] | Variant of the ScanningSequence. Corresponds to DICOM Tag 0018, 0021 `Sequence Variant`.                                                                                                                                                                                  |
-| ScanOptions                 | RECOMMENDED                                                 | [string][] or [array][] of [strings][] | Parameters of ScanningSequence. Corresponds to DICOM Tag 0018, 0022 `Scan Options`.                                                                                                                                                                                       |
-| SequenceName                | RECOMMENDED                                                 | [string][]                             | Manufacturer's designation of the sequence name. Corresponds to DICOM Tag 0018, 0024 `Sequence Name`.                                                                                                                                                                     |
-| PulseSequenceDetails        | RECOMMENDED                                                 | [string][]                             | Information beyond pulse sequence type that identifies the specific pulse sequence used (for example, "Standard Siemens Sequence distributed with the VB17 software," "Siemens WIP ### version #.##," or "Sequence written by X using a version compiled on MM/DD/YYYY"). |
-| NonlinearGradientCorrection | RECOMMENDED                                                 | [boolean][]                            | Boolean stating if the image saved has been corrected for gradient nonlinearities by the scanner sequence.                                                                                                                                                                |
-| MTState                     | RECOMMENDED                                                 | [boolean][]                            | Boolean stating whether the magnetization transfer pulse is applied. Corresponds to DICOM tag (0018, 9020) `Magnetization Transfer`.                                                                                                                                      |
-| MTOffsetFrequency           | RECOMMENDED if the MTstate is `True`.                       | [number][]                             | The frequency offset of the magnetization transfer pulse with respect to the central H1 Larmor frequency in Hertz (Hz).                                                                                                                                                   |
-| MTPulseBandwidth            | RECOMMENDED if the MTstate is `True`.                       | [number][]                             | The excitation bandwidth of the magnetization transfer pulse in Hertz (Hz).                                                                                                                                                                                               |
-| MTNumberOfPulses            | RECOMMENDED if the MTstate is `True`.                       | [number][]                             | The number of magnetization transfer RF pulses applied before the readout.                                                                                                                                                                                         |
-| MTPulseShape                | RECOMMENDED if the MTstate is `True`.                       | [string][]                             | Shape of the magnetization transfer RF pulse waveform. Accepted values: `HARD`, `GAUSSIAN`, `GAUSSHANN` (gaussian pulse with Hanning window), `SINC`, `SINCHANN` (sinc pulse with Hanning window), `SINCGAUSS` (sinc pulse with Gaussian window), `FERMI`.                |
-| MTPulseDuration             | RECOMMENDED if the MTstate is `True`.                       | [number][]                             | Duration of the magnetization transfer RF pulse in seconds.                                                                                                                                                                                          |
-| SpoilingState               | RECOMMENDED                                                 | [boolean][]                            | Boolean stating whether the pulse sequence uses any type of spoiling strategy to suppress residual transverse magnetization.                                                                                                                                           |
-| SpoilingType                | RECOMMENDED if the SpoilingState is `True`.                 | [string][]                             | Specifies which spoiling method(s) are used by a spoiled sequence. Accepted values: `RF`, `GRADIENT` or `COMBINED`.                                                                                                                                                  |
-| SpoilingRFPhaseIncrement    | RECOMMENDED if the SpoilingType is `RF` or `COMBINED`.      | [number][]                             | The amount of incrementation described in degrees, which is applied to the phase of the excitation pulse at each TR period for achieving RF spoiling.                                                                                                                        |
-| SpoilingGradientMoment      | RECOMMENDED if the SpoilingType is `GRADIENT` or `COMBINED`. | [number][]                            | Zeroth moment of the spoiler gradient lobe in millitesla times second per meter (mT.s/m).                                                                                                                                                                                   |
-| SpoilingGradientDuration    | RECOMMENDED if the SpoilingType is `GRADIENT` or `COMBINED`. | [number][]                            | The duration of the spoiler gradient lobe in seconds. The duration of a trapezoidal lobe is defined as the summation of ramp-up and plateu times.                                                                                                                                                                                            |
+| **Key name**                | **Requirement level**                                        | **Data type**                          | **Description**                                                                                                                                                                                                                                                           |
+|-----------------------------|--------------------------------------------------------------|----------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| PulseSequenceType           | RECOMMENDED                                                  | [string][]                             | A general description of the pulse sequence used for the scan (for example, MPRAGE, Gradient Echo EPI, Spin Echo EPI, Multiband gradient echo EPI).                                                                                                                       |
+| ScanningSequence            | RECOMMENDED                                                  | [string][] or [array][] of [strings][] | Description of the type of data acquired. Corresponds to DICOM Tag 0018, 0020 `Scanning Sequence`.                                                                                                                                                                        |
+| SequenceVariant             | RECOMMENDED                                                  | [string][] or [array][] of [strings][] | Variant of the ScanningSequence. Corresponds to DICOM Tag 0018, 0021 `Sequence Variant`.                                                                                                                                                                                  |
+| ScanOptions                 | RECOMMENDED                                                  | [string][] or [array][] of [strings][] | Parameters of ScanningSequence. Corresponds to DICOM Tag 0018, 0022 `Scan Options`.                                                                                                                                                                                       |
+| SequenceName                | RECOMMENDED                                                  | [string][]                             | Manufacturer's designation of the sequence name. Corresponds to DICOM Tag 0018, 0024 `Sequence Name`.                                                                                                                                                                     |
+| PulseSequenceDetails        | RECOMMENDED                                                  | [string][]                             | Information beyond pulse sequence type that identifies the specific pulse sequence used (for example, "Standard Siemens Sequence distributed with the VB17 software," "Siemens WIP ### version #.##," or "Sequence written by X using a version compiled on MM/DD/YYYY"). |
+| NonlinearGradientCorrection | RECOMMENDED                                                  | [boolean][]                            | Boolean stating if the image saved has been corrected for gradient nonlinearities by the scanner sequence.                                                                                                                                                                |
+| MTState                     | RECOMMENDED                                                  | [boolean][]                            | Boolean stating whether the magnetization transfer pulse is applied. Corresponds to DICOM tag (0018, 9020) `Magnetization Transfer`.                                                                                                                                      |
+| MTOffsetFrequency           | RECOMMENDED if the MTstate is `True`.                        | [number][]                             | The frequency offset of the magnetization transfer pulse with respect to the central H1 Larmor frequency in Hertz (Hz).                                                                                                                                                   |
+| MTPulseBandwidth            | RECOMMENDED if the MTstate is `True`.                        | [number][]                             | The excitation bandwidth of the magnetization transfer pulse in Hertz (Hz).                                                                                                                                                                                               |
+| MTNumberOfPulses            | RECOMMENDED if the MTstate is `True`.                        | [number][]                             | The number of magnetization transfer RF pulses applied before the readout.                                                                                                                                                                                                |
+| MTPulseShape                | RECOMMENDED if the MTstate is `True`.                        | [string][]                             | Shape of the magnetization transfer RF pulse waveform. Accepted values: `HARD`, `GAUSSIAN`, `GAUSSHANN` (gaussian pulse with Hanning window), `SINC`, `SINCHANN` (sinc pulse with Hanning window), `SINCGAUSS` (sinc pulse with Gaussian window), `FERMI`.                |
+| MTPulseDuration             | RECOMMENDED if the MTstate is `True`.                        | [number][]                             | Duration of the magnetization transfer RF pulse in seconds.                                                                                                                                                                                                               |
+| SpoilingState               | RECOMMENDED                                                  | [boolean][]                            | Boolean stating whether the pulse sequence uses any type of spoiling strategy to suppress residual transverse magnetization.                                                                                                                                              |
+| SpoilingType                | RECOMMENDED if the SpoilingState is `True`.                  | [string][]                             | Specifies which spoiling method(s) are used by a spoiled sequence. Accepted values: `RF`, `GRADIENT` or `COMBINED`.                                                                                                                                                       |
+| SpoilingRFPhaseIncrement    | RECOMMENDED if the SpoilingType is `RF` or `COMBINED`.       | [number][]                             | The amount of incrementation described in degrees, which is applied to the phase of the excitation pulse at each TR period for achieving RF spoiling.                                                                                                                     |
+| SpoilingGradientMoment      | RECOMMENDED if the SpoilingType is `GRADIENT` or `COMBINED`. | [number][]                             | Zeroth moment of the spoiler gradient lobe in millitesla times second per meter (mT.s/m).                                                                                                                                                                                 |
+| SpoilingGradientDuration    | RECOMMENDED if the SpoilingType is `GRADIENT` or `COMBINED`. | [number][]                             | The duration of the spoiler gradient lobe in seconds. The duration of a trapezoidal lobe is defined as the summation of ramp-up and plateu times.                                                                                                                         |
 
 ### In-Plane Spatial Encoding
-| **Key name**                   | **Requirement level** | **Data type** | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
-|--------------------------------|-----------------------|---------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| NumberShots                    | RECOMMENDED           | [number][] or [array][] of [numbers]    | The number of RF excitations needed to reconstruct a slice or volume (may be referred to as partition). Please mind that this is not the same as Echo Train Length which denotes the number of k-space lines collected after excitation in a multi-echo readout. The data type array is applicable for specifying this parameter before and after the k-space center is sampled. Plase see [`NumberShots` metadata field](../99-appendices/11-qmri.md#numbershots-metadata-field) in the qMRI appendix for corresponding calculations.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
-| ParallelReductionFactorInPlane | RECOMMENDED           | [number][]    | The parallel imaging (for instance, GRAPPA) factor. Use the denominator of the fraction of k-space encoded for each slice. For example, 2 means half of k-space is encoded. Corresponds to DICOM Tag 0018, 9069 `Parallel Reduction Factor In-plane`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
-| ParallelAcquisitionTechnique   | RECOMMENDED           | [string][]    | The type of parallel imaging used (for example GRAPPA, SENSE). Corresponds to DICOM Tag 0018, 9078 `Parallel Acquisition Technique`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
-| PartialFourier                 | RECOMMENDED           | [number][]    | The fraction of partial Fourier information collected. Corresponds to DICOM Tag 0018, 9081 `Partial Fourier`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
-| PartialFourierDirection        | RECOMMENDED           | [string][]    | The direction where only partial Fourier information was collected. Corresponds to DICOM Tag 0018, 9036 `Partial Fourier Direction`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
-| PhaseEncodingDirection         | RECOMMENDED           | [string][]    | Possible values: `i`, `j`, `k`, `i-`, `j-`, `k-`. The letters `i`, `j`, `k` correspond to the first, second and third axis of the data in the NIFTI file. The polarity of the phase encoding is assumed to go from zero index to maximum index unless `-` sign is present (then the order is reversed - starting from the highest index instead of zero). `PhaseEncodingDirection` is defined as the direction along which phase is was modulated which may result in visible distortions. Note that this is not the same as the DICOM term `InPlanePhaseEncodingDirection` which can have `ROW` or `COL` values. This parameter is REQUIRED if corresponding fieldmap data is present or when using multiple runs with different phase encoding directions (which can be later used for field inhomogeneity correction). |
-| EffectiveEchoSpacing           | RECOMMENDED           | [number][]    | The "effective" sampling interval, specified in seconds, between lines in the phase-encoding direction, defined based on the size of the reconstructed image in the phase direction. It is frequently, but incorrectly, referred to as "dwell time" (see `DwellTime` parameter below for actual dwell time). It is required for unwarping distortions using field maps. Note that beyond just in-plane acceleration, a variety of other manipulations to the phase encoding need to be accounted for properly, including partial fourier, phase oversampling, phase resolution, phase field-of-view and interpolation.<sup>2</sup> This parameter is REQUIRED if corresponding fieldmap data is present.                                                                                                                  |
-| TotalReadoutTime               | RECOMMENDED           | [number][]    | This is actually the "effective" total readout time , defined as the readout duration, specified in seconds, that would have generated data with the given level of distortion. It is NOT the actual, physical duration of the readout train. If `EffectiveEchoSpacing` has been properly computed, it is just `EffectiveEchoSpacing * (ReconMatrixPE - 1)`.<sup>3</sup> . This parameter is REQUIRED if corresponding "field/distortion" maps acquired with opposing phase encoding directions are present (see 8.9.4).                                                                                                                                                                                                                                                                                                  |
-| MixingTime                     | RECOMMENDED           | [number][]    | In the context of a stimulated- and spin-echo 3D EPI sequence for B1+ mapping, corresponds to the interval between spin- and stimulated-echo pulses. In the context of a diffusion-weighted double spin-echo sequence, corresponds to the interval between two successive diffusion sensitizing gradients, specified in seconds.                                                                                                                                                                                                                                                                                            |
+| **Key name**                   | **Requirement level** | **Data type**                        | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
+|--------------------------------|-----------------------|--------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| NumberShots                    | RECOMMENDED           | [number][] or [array][] of [numbers] | The number of RF excitations needed to reconstruct a slice or volume (may be referred to as partition). Please mind that this is not the same as Echo Train Length which denotes the number of k-space lines collected after excitation in a multi-echo readout. The data type array is applicable for specifying this parameter before and after the k-space center is sampled. Plase see [`NumberShots` metadata field](../99-appendices/11-qmri.md#numbershots-metadata-field) in the qMRI appendix for corresponding calculations.                                                                                                                                                                                                                                                                                    |
+| ParallelReductionFactorInPlane | RECOMMENDED           | [number][]                           | The parallel imaging (for instance, GRAPPA) factor. Use the denominator of the fraction of k-space encoded for each slice. For example, 2 means half of k-space is encoded. Corresponds to DICOM Tag 0018, 9069 `Parallel Reduction Factor In-plane`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
+| ParallelAcquisitionTechnique   | RECOMMENDED           | [string][]                           | The type of parallel imaging used (for example GRAPPA, SENSE). Corresponds to DICOM Tag 0018, 9078 `Parallel Acquisition Technique`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+| PartialFourier                 | RECOMMENDED           | [number][]                           | The fraction of partial Fourier information collected. Corresponds to DICOM Tag 0018, 9081 `Partial Fourier`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
+| PartialFourierDirection        | RECOMMENDED           | [string][]                           | The direction where only partial Fourier information was collected. Corresponds to DICOM Tag 0018, 9036 `Partial Fourier Direction`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+| PhaseEncodingDirection         | RECOMMENDED           | [string][]                           | Possible values: `i`, `j`, `k`, `i-`, `j-`, `k-`. The letters `i`, `j`, `k` correspond to the first, second and third axis of the data in the NIFTI file. The polarity of the phase encoding is assumed to go from zero index to maximum index unless `-` sign is present (then the order is reversed - starting from the highest index instead of zero). `PhaseEncodingDirection` is defined as the direction along which phase is was modulated which may result in visible distortions. Note that this is not the same as the DICOM term `InPlanePhaseEncodingDirection` which can have `ROW` or `COL` values. This parameter is REQUIRED if corresponding fieldmap data is present or when using multiple runs with different phase encoding directions (which can be later used for field inhomogeneity correction). |
+| EffectiveEchoSpacing           | RECOMMENDED           | [number][]                           | The "effective" sampling interval, specified in seconds, between lines in the phase-encoding direction, defined based on the size of the reconstructed image in the phase direction. It is frequently, but incorrectly, referred to as "dwell time" (see `DwellTime` parameter below for actual dwell time). It is required for unwarping distortions using field maps. Note that beyond just in-plane acceleration, a variety of other manipulations to the phase encoding need to be accounted for properly, including partial fourier, phase oversampling, phase resolution, phase field-of-view and interpolation.<sup>2</sup> This parameter is REQUIRED if corresponding fieldmap data is present.                                                                                                                  |
+| TotalReadoutTime               | RECOMMENDED           | [number][]                           | This is actually the "effective" total readout time , defined as the readout duration, specified in seconds, that would have generated data with the given level of distortion. It is NOT the actual, physical duration of the readout train. If `EffectiveEchoSpacing` has been properly computed, it is just `EffectiveEchoSpacing * (ReconMatrixPE - 1)`.<sup>3</sup> . This parameter is REQUIRED if corresponding "field/distortion" maps acquired with opposing phase encoding directions are present (see 8.9.4).                                                                                                                                                                                                                                                                                                  |
+| MixingTime                     | RECOMMENDED           | [number][]                           | In the context of a stimulated- and spin-echo 3D EPI sequence for B1+ mapping, corresponds to the interval between spin- and stimulated-echo pulses. In the context of a diffusion-weighted double spin-echo sequence, corresponds to the interval between two successive diffusion sensitizing gradients, specified in seconds.                                                                                                                                                                                                                                                                                            |
 
 <sup>2</sup>Conveniently, for Siemens data, this value is easily obtained as
 `1 / (BWPPPE * ReconMatrixPE)`, where BWPPPE is the
@@ -146,16 +146,16 @@ sub-<label>/[ses-<label>/]
 Anatomical (structural) data acquired for that participant. Currently supported
 non-parametric structural MR images include:
 
-| **Name**                                   | `suffix`         | **Description**                                                                                                                                   |
-| ------------------------------------------ | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- |
-| T1 weighted images                         | T1w              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the longitudinal relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively short repetition and echo times. To achieve this weighting in gradient-echo images, again, short repetition and echo times are selected; however, at relatively large flip angles. Another common approach to increase T1 weighting in gradient-echo images is to add an inversion preparation block to the beginning of the imaging sequence (for example, `TurboFLASH` or `MP-RAGE`).                           |
-| T2 weighted images                         | T2w              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the (true) transverse relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively long repetition and echo times. Generally, gradient echo sequences are not the most suitable option for achieving T2 weighting, as their contrast natively depends on T2-star rather than on T2.        |
-| Proton density (PD) weighted images        | PDw              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the spin density (1H) of the imaged specimen. In spin-echo sequences this contrast is achieved at short repetition and long echo times. In a gradient-echo acquisition, PD weighting dominates the contrast at long repetition and short echo times, and at small flip angles.|
-| T2star weighted images                     | T2starw          | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the (observed) transverse relaxation time of the imaged specimen. In spin-echo sequences, this effect is negated as the excitation is followed by an inversion pulse. The contrast of gradient-echo images natively depends on T2-star effects. However, for T2-star variation to dominate the image contrast, gradient-echo acquisitions are carried out at long repetition and echo times, and at small flip angles.                                                                                                     |
-| Fluid attenuated inversion recovery images | FLAIR            | In arbitrary units (arbitrary). Structural images with predominant T2 contribution (a.k.a T2-FLAIR), in which signal from fluids (for example, CSF) is nulled out by adjusting inversion time, coupled with notably long repetition and echo times.                                                  |
-| Inplane T1                                 | inplaneT1        | In arbitrary units (arbitrary). T1 weighted structural image matched to a functional (task) image.                                                                                  |
-| Inplane T2                                 | inplaneT2        | In arbitrary units (arbitrary). T2 weighted structural image matched to a functional (task) image.                                                                                  |
-| PD and T2 weighted images                  | PDT2             | In arbitrary units (arbitrary). PDw and T2w images acquired using a dual echo FSE sequence through view sharing process ([Johnson et al. 1994](https://pubmed.ncbi.nlm.nih.gov/8010268/)).                                      |
+| **Name**                                   | `suffix`         | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
+| ------------------------------------------ | ---------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| T1 weighted images                         | T1w              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the longitudinal relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively short repetition and echo times. To achieve this weighting in gradient-echo images, again, short repetition and echo times are selected; however, at relatively large flip angles. Another common approach to increase T1 weighting in gradient-echo images is to add an inversion preparation block to the beginning of the imaging sequence (for example, `TurboFLASH` or `MP-RAGE`). |
+| T2 weighted images                         | T2w              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the (true) transverse relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively long repetition and echo times. Generally, gradient echo sequences are not the most suitable option for achieving T2 weighting, as their contrast natively depends on T2-star rather than on T2.                                                                                                                                                                                   |
+| Proton density (PD) weighted images        | PDw              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the spin density (1H) of the imaged specimen. In spin-echo sequences this contrast is achieved at short repetition and long echo times. In a gradient-echo acquisition, PD weighting dominates the contrast at long repetition and short echo times, and at small flip angles.                                                                                                                                                                                                                                  |
+| T2star weighted images                     | T2starw          | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the (observed) transverse relaxation time of the imaged specimen. In spin-echo sequences, this effect is negated as the excitation is followed by an inversion pulse. The contrast of gradient-echo images natively depends on T2-star effects. However, for T2-star variation to dominate the image contrast, gradient-echo acquisitions are carried out at long repetition and echo times, and at small flip angles.                                                                                          |
+| Fluid attenuated inversion recovery images | FLAIR            | In arbitrary units (arbitrary). Structural images with predominant T2 contribution (a.k.a T2-FLAIR), in which signal from fluids (for example, CSF) is nulled out by adjusting inversion time, coupled with notably long repetition and echo times.                                                                                                                                                                                                                                                                                                                                                                        |
+| Inplane T1                                 | inplaneT1        | In arbitrary units (arbitrary). T1 weighted structural image matched to a functional (task) image.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
+| Inplane T2                                 | inplaneT2        | In arbitrary units (arbitrary). T2 weighted structural image matched to a functional (task) image.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
+| PD and T2 weighted images                  | PDT2             | In arbitrary units (arbitrary). PDw and T2w images acquired using a dual echo FSE sequence through view sharing process ([Johnson et al. 1994](https://pubmed.ncbi.nlm.nih.gov/8010268/)).                                                                                                                                                                                                                                                                                                                                                                                                                                 |
 
 If the structural images included in the dataset were defaced (to protect
 identity of participants) one MAY provide the binary mask that was used to
@@ -244,24 +244,24 @@ constitute parametric maps. Currently supported parametric maps include:
 | **Name**                                     | `suffix`  | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
 |----------------------------------------------|-----------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
 | Longitudinal relaxation time map             | T1map     | In seconds (s). T1 maps are REQUIRED to use this suffix regardless of the method used to generate them. See [this interactive book on T1 mapping](https://qmrlab.org/t1_book/intro) for further reading on T1-mapping.                                                                                                                                                                                                                                                                                            |
-| Longitudinal relaxation rate map             | R1map     | In seconds<sup>-1</sup> (1/s). R1 maps (R1 = 1/T1) are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                            |
+| Longitudinal relaxation rate map             | R1map     | In seconds<sup>-1</sup> (1/s). R1 maps (R1 = 1/T1) are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                |
 | True transverse relaxation time map          | T2map     | In seconds (s). T2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                                           |
-| True transverse relaxation rate map          | R2map     | In seconds<sup>-1</sup> (1/s). R2 maps (R2 = 1/T2) are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                            |
+| True transverse relaxation rate map          | R2map     | In seconds<sup>-1</sup> (1/s). R2 maps (R2 = 1/T2) are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                |
 | Observed transverse relaxation time map      | T2starmap | In seconds (s). T2-star maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                                      |
-| Observed transverse relaxation rate map      | R2starmap | In seconds<sup>-1</sup> (1/s). R2-star maps (R2star = 1/T2star) are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                       |
+| Observed transverse relaxation rate map      | R2starmap | In seconds<sup>-1</sup> (1/s). R2-star maps (R2star = 1/T2star) are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                   |
 | Proton density map                           | PDmap     | In arbitrary units (arbitrary). PD maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                           |
-| Magnetization transfer ratio map             | MTRmap    | In arbitrary units (arbitrary). MTR maps are REQUIRED to use this suffix regardless of the method used to generate them. MTRmap intensity values are RECOMMENDED to be represented in percentage in the range of 0-100%.                                                                                                                                                                                                                                                                                                                                                                                                       |
+| Magnetization transfer ratio map             | MTRmap    | In arbitrary units (arbitrary). MTR maps are REQUIRED to use this suffix regardless of the method used to generate them. MTRmap intensity values are RECOMMENDED to be represented in percentage in the range of 0-100%.                                                                                                                                                                                                                                                                                          |
 | Magnetization transfer saturation map        | MTsat     | In arbitrary units (arbitrary). MTsat maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                        |
 | Homogeneous (flat) T1-weighted MP2RAGE image | UNIT1     | In arbitrary units (arbitrary). UNIT1 images are REQUIRED to use this suffix regardless of the method used to generate them. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from from `T1w`.                                                                                                                                                        |
 | T1 in rotating frame (T1 rho) map            | T1rho     | In seconds (s). T1-rho maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                                       |
-| Myelin water fraction map                    | MWFmap    | In arbitrary units (arbitrary). MWF maps are REQUIRED to use this suffix regardless of the method used to generate them. MWF intensity values are RECOMMENDED to be represented in percentage in the range of 0-100%.                                                                                                                                                                                                                                                                                                                                                                                                       |
+| Myelin water fraction map                    | MWFmap    | In arbitrary units (arbitrary). MWF maps are REQUIRED to use this suffix regardless of the method used to generate them. MWF intensity values are RECOMMENDED to be represented in percentage in the range of 0-100%.                                                                                                                                                                                                                                                                                             |
 | Macromolecular tissue volume (MTV) map       | MTVmap    | In arbitrary units (arbitrary). MTV maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                          |
 | Combined PD/T2 map                           | PDT2map   | In arbitrary units (arbitrary). Combined PD/T2 maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                               |
 | Quantitative susceptibility map (QSM)        | Chimap    | In parts per million (ppm). QSM allows for determining the underlying magnetic susceptibility of tissue (Chi) ([Wang & Liu, 2014](https://onlinelibrary.wiley.com/doi/10.1002/mrm.25358)). Chi maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                               |
-| RF transmit field map                        | TB1map    | In arbitrary units (arbitrary). Radio frequency (RF) transmit (B1+) field maps are REQUIRED to use this suffix regardless of the method used to generate them. TB1map intensity values are RECOMMENDED to be represented as percent multiplicative factors such that FlipAngle<sub>effective</sub> = B1+<sub>intensity</sub>*FlipAngle<sub>nominal</sub> .                                                                                                                                                                                                                                                                                                                                                                    |
-| RF receive sensitivity map                   | RB1map    | In arbitrary units (arbitrary). Radio frequency (RF) receive (B1-) sensitivity maps are REQUIRED to use this suffix regardless of the method used to generate them. RB1map intensity values are RECOMMENDED to be represented as percent multiplicative factors such that Amplitude<sub>effective</sub> = B1-<sub>intensity</sub>*Amplitude<sub>ideal</sub>.                                                                                                                                                                                                                                                                                                                                                            |
+| RF transmit field map                        | TB1map    | In arbitrary units (arbitrary). Radio frequency (RF) transmit (B1+) field maps are REQUIRED to use this suffix regardless of the method used to generate them. TB1map intensity values are RECOMMENDED to be represented as percent multiplicative factors such that FlipAngle<sub>effective</sub> = B1+<sub>intensity</sub>\*FlipAngle<sub>nominal</sub> .                                                                                                                                                       |
+| RF receive sensitivity map                   | RB1map    | In arbitrary units (arbitrary). Radio frequency (RF) receive (B1-) sensitivity maps are REQUIRED to use this suffix regardless of the method used to generate them. RB1map intensity values are RECOMMENDED to be represented as percent multiplicative factors such that Amplitude<sub>effective</sub> = B1-<sub>intensity</sub>\*Amplitude<sub>ideal</sub>.                                                                                                                                                     |
 | Observed signal amplitude (S0) map           | S0map     | In arbitrary units (arbitrary). For a multi-echo (typically fMRI) sequence, S0 maps index the baseline signal before exponential (T2-star) signal decay. In other words: the exponential of the intercept for a linear decay model across log-transformed echos. For more information, please see, for example, [the tedana documentation](https://tedana.readthedocs.io/en/latest/approach.html#monoexponential-decay-model-fit). S0 maps are RECOMMENDED to use this suffix if derived from an ME-FMRI dataset. |
-| Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (arbitrary). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications (for example, variable flip angle T1 mapping.                                                                                                                                                                                                                                          |
+| Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (arbitrary). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications (for example, variable flip angle T1 mapping.                                                                                                                                                                                                                                  |
 
 Parametric images listed in the table above are typically generated by
 processing a [file collection](../02-common-principles.md#entity-linked-file-collections).
@@ -284,7 +284,7 @@ They are, however, still valid suffixes, to maintain backwards compatibility.
 The following suffixes are valid, but SHOULD NOT be used for new BIDS compatible
 datasets (created after version 1.5.0.):
 
-| **Name**           | `suffix` | **Reason to deprecate**                                                                                                                                                                                                                                                                                                                                                                                                                    |
+| **Name**           | `suffix`         | **Reason to deprecate**                                                                                                                                                                                                                                                                                                                                                                                                                    |
 | ------------------ | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
 | T2\*               | T2star           | Ambiguous, may refer to a parametric image or to a conventional image. **Change:** Replaced by `T2starw` or `T2starmap`.                                                                                                                                                                                                                                                                                                                   |
 | FLASH              | FLASH            | FLASH (Fast-Low-Angle-Shot) is a vendor specific implementation for spoiled gradient echo acquisition. It is commonly used for rapid anatomical imaging and also for many different qMRI applications. When used for a single file, it does not convey any information about the image contrast. When used in a file collection, it may result in conflicts across filenames of different applications. **Change:** Removed from suffixes. |

From 027b32429c9c85112265ac72e459f8b479bced37 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 6 Jan 2021 11:39:14 -0500
Subject: [PATCH 74/83] STY: Fix link syntax, one more table fence

---
 .../01-magnetic-resonance-imaging-data.md     | 22 +++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 4adaf42cd9..1014a85cf4 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -65,17 +65,17 @@ that a given scan was collected with the intended coil elements selected
 | SpoilingGradientDuration    | RECOMMENDED if the SpoilingType is `GRADIENT` or `COMBINED`. | [number][]                             | The duration of the spoiler gradient lobe in seconds. The duration of a trapezoidal lobe is defined as the summation of ramp-up and plateu times.                                                                                                                         |
 
 ### In-Plane Spatial Encoding
-| **Key name**                   | **Requirement level** | **Data type**                        | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
-|--------------------------------|-----------------------|--------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| NumberShots                    | RECOMMENDED           | [number][] or [array][] of [numbers] | The number of RF excitations needed to reconstruct a slice or volume (may be referred to as partition). Please mind that this is not the same as Echo Train Length which denotes the number of k-space lines collected after excitation in a multi-echo readout. The data type array is applicable for specifying this parameter before and after the k-space center is sampled. Plase see [`NumberShots` metadata field](../99-appendices/11-qmri.md#numbershots-metadata-field) in the qMRI appendix for corresponding calculations.                                                                                                                                                                                                                                                                                    |
-| ParallelReductionFactorInPlane | RECOMMENDED           | [number][]                           | The parallel imaging (for instance, GRAPPA) factor. Use the denominator of the fraction of k-space encoded for each slice. For example, 2 means half of k-space is encoded. Corresponds to DICOM Tag 0018, 9069 `Parallel Reduction Factor In-plane`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
-| ParallelAcquisitionTechnique   | RECOMMENDED           | [string][]                           | The type of parallel imaging used (for example GRAPPA, SENSE). Corresponds to DICOM Tag 0018, 9078 `Parallel Acquisition Technique`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
-| PartialFourier                 | RECOMMENDED           | [number][]                           | The fraction of partial Fourier information collected. Corresponds to DICOM Tag 0018, 9081 `Partial Fourier`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
-| PartialFourierDirection        | RECOMMENDED           | [string][]                           | The direction where only partial Fourier information was collected. Corresponds to DICOM Tag 0018, 9036 `Partial Fourier Direction`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
-| PhaseEncodingDirection         | RECOMMENDED           | [string][]                           | Possible values: `i`, `j`, `k`, `i-`, `j-`, `k-`. The letters `i`, `j`, `k` correspond to the first, second and third axis of the data in the NIFTI file. The polarity of the phase encoding is assumed to go from zero index to maximum index unless `-` sign is present (then the order is reversed - starting from the highest index instead of zero). `PhaseEncodingDirection` is defined as the direction along which phase is was modulated which may result in visible distortions. Note that this is not the same as the DICOM term `InPlanePhaseEncodingDirection` which can have `ROW` or `COL` values. This parameter is REQUIRED if corresponding fieldmap data is present or when using multiple runs with different phase encoding directions (which can be later used for field inhomogeneity correction). |
-| EffectiveEchoSpacing           | RECOMMENDED           | [number][]                           | The "effective" sampling interval, specified in seconds, between lines in the phase-encoding direction, defined based on the size of the reconstructed image in the phase direction. It is frequently, but incorrectly, referred to as "dwell time" (see `DwellTime` parameter below for actual dwell time). It is required for unwarping distortions using field maps. Note that beyond just in-plane acceleration, a variety of other manipulations to the phase encoding need to be accounted for properly, including partial fourier, phase oversampling, phase resolution, phase field-of-view and interpolation.<sup>2</sup> This parameter is REQUIRED if corresponding fieldmap data is present.                                                                                                                  |
-| TotalReadoutTime               | RECOMMENDED           | [number][]                           | This is actually the "effective" total readout time , defined as the readout duration, specified in seconds, that would have generated data with the given level of distortion. It is NOT the actual, physical duration of the readout train. If `EffectiveEchoSpacing` has been properly computed, it is just `EffectiveEchoSpacing * (ReconMatrixPE - 1)`.<sup>3</sup> . This parameter is REQUIRED if corresponding "field/distortion" maps acquired with opposing phase encoding directions are present (see 8.9.4).                                                                                                                                                                                                                                                                                                  |
-| MixingTime                     | RECOMMENDED           | [number][]                           | In the context of a stimulated- and spin-echo 3D EPI sequence for B1+ mapping, corresponds to the interval between spin- and stimulated-echo pulses. In the context of a diffusion-weighted double spin-echo sequence, corresponds to the interval between two successive diffusion sensitizing gradients, specified in seconds.                                                                                                                                                                                                                                                                                            |
+| **Key name**                   | **Requirement level** | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
+|--------------------------------|-----------------------|----------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| NumberShots                    | RECOMMENDED           | [number][] or [array][] of [numbers][] | The number of RF excitations needed to reconstruct a slice or volume (may be referred to as partition). Please mind that this is not the same as Echo Train Length which denotes the number of k-space lines collected after excitation in a multi-echo readout. The data type array is applicable for specifying this parameter before and after the k-space center is sampled. Plase see [`NumberShots` metadata field](../99-appendices/11-qmri.md#numbershots-metadata-field) in the qMRI appendix for corresponding calculations.                                                                                                                                                                                                                                                                                    |
+| ParallelReductionFactorInPlane | RECOMMENDED           | [number][]                             | The parallel imaging (for instance, GRAPPA) factor. Use the denominator of the fraction of k-space encoded for each slice. For example, 2 means half of k-space is encoded. Corresponds to DICOM Tag 0018, 9069 `Parallel Reduction Factor In-plane`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
+| ParallelAcquisitionTechnique   | RECOMMENDED           | [string][]                             | The type of parallel imaging used (for example GRAPPA, SENSE). Corresponds to DICOM Tag 0018, 9078 `Parallel Acquisition Technique`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+| PartialFourier                 | RECOMMENDED           | [number][]                             | The fraction of partial Fourier information collected. Corresponds to DICOM Tag 0018, 9081 `Partial Fourier`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
+| PartialFourierDirection        | RECOMMENDED           | [string][]                             | The direction where only partial Fourier information was collected. Corresponds to DICOM Tag 0018, 9036 `Partial Fourier Direction`.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+| PhaseEncodingDirection         | RECOMMENDED           | [string][]                             | Possible values: `i`, `j`, `k`, `i-`, `j-`, `k-`. The letters `i`, `j`, `k` correspond to the first, second and third axis of the data in the NIFTI file. The polarity of the phase encoding is assumed to go from zero index to maximum index unless `-` sign is present (then the order is reversed - starting from the highest index instead of zero). `PhaseEncodingDirection` is defined as the direction along which phase is was modulated which may result in visible distortions. Note that this is not the same as the DICOM term `InPlanePhaseEncodingDirection` which can have `ROW` or `COL` values. This parameter is REQUIRED if corresponding fieldmap data is present or when using multiple runs with different phase encoding directions (which can be later used for field inhomogeneity correction). |
+| EffectiveEchoSpacing           | RECOMMENDED           | [number][]                             | The "effective" sampling interval, specified in seconds, between lines in the phase-encoding direction, defined based on the size of the reconstructed image in the phase direction. It is frequently, but incorrectly, referred to as "dwell time" (see `DwellTime` parameter below for actual dwell time). It is required for unwarping distortions using field maps. Note that beyond just in-plane acceleration, a variety of other manipulations to the phase encoding need to be accounted for properly, including partial fourier, phase oversampling, phase resolution, phase field-of-view and interpolation.<sup>2</sup> This parameter is REQUIRED if corresponding fieldmap data is present.                                                                                                                  |
+| TotalReadoutTime               | RECOMMENDED           | [number][]                             | This is actually the "effective" total readout time , defined as the readout duration, specified in seconds, that would have generated data with the given level of distortion. It is NOT the actual, physical duration of the readout train. If `EffectiveEchoSpacing` has been properly computed, it is just `EffectiveEchoSpacing * (ReconMatrixPE - 1)`.<sup>3</sup> . This parameter is REQUIRED if corresponding "field/distortion" maps acquired with opposing phase encoding directions are present (see 8.9.4).                                                                                                                                                                                                                                                                                                  |
+| MixingTime                     | RECOMMENDED           | [number][]                             | In the context of a stimulated- and spin-echo 3D EPI sequence for B1+ mapping, corresponds to the interval between spin- and stimulated-echo pulses. In the context of a diffusion-weighted double spin-echo sequence, corresponds to the interval between two successive diffusion sensitizing gradients, specified in seconds.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
 
 <sup>2</sup>Conveniently, for Siemens data, this value is easily obtained as
 `1 / (BWPPPE * ReconMatrixPE)`, where BWPPPE is the

From 2fbcc57aa31211406476d2db8ac9be2131bcef41 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 6 Jan 2021 11:41:19 -0500
Subject: [PATCH 75/83] Fix typo

---
 .../01-magnetic-resonance-imaging-data.md                       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 1014a85cf4..ad9ee0b834 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -62,7 +62,7 @@ that a given scan was collected with the intended coil elements selected
 | SpoilingType                | RECOMMENDED if the SpoilingState is `True`.                  | [string][]                             | Specifies which spoiling method(s) are used by a spoiled sequence. Accepted values: `RF`, `GRADIENT` or `COMBINED`.                                                                                                                                                       |
 | SpoilingRFPhaseIncrement    | RECOMMENDED if the SpoilingType is `RF` or `COMBINED`.       | [number][]                             | The amount of incrementation described in degrees, which is applied to the phase of the excitation pulse at each TR period for achieving RF spoiling.                                                                                                                     |
 | SpoilingGradientMoment      | RECOMMENDED if the SpoilingType is `GRADIENT` or `COMBINED`. | [number][]                             | Zeroth moment of the spoiler gradient lobe in millitesla times second per meter (mT.s/m).                                                                                                                                                                                 |
-| SpoilingGradientDuration    | RECOMMENDED if the SpoilingType is `GRADIENT` or `COMBINED`. | [number][]                             | The duration of the spoiler gradient lobe in seconds. The duration of a trapezoidal lobe is defined as the summation of ramp-up and plateu times.                                                                                                                         |
+| SpoilingGradientDuration    | RECOMMENDED if the SpoilingType is `GRADIENT` or `COMBINED`. | [number][]                             | The duration of the spoiler gradient lobe in seconds. The duration of a trapezoidal lobe is defined as the summation of ramp-up and plateau times.                                                                                                                         |
 
 ### In-Plane Spatial Encoding
 | **Key name**                   | **Requirement level** | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |

From d3084f65cc979f3358203e4a940f15ec1070dd65 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Wed, 6 Jan 2021 11:43:29 -0500
Subject: [PATCH 76/83] Fix paranthesis

---
 .../01-magnetic-resonance-imaging-data.md                       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index ad9ee0b834..09db9b28d9 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -261,7 +261,7 @@ constitute parametric maps. Currently supported parametric maps include:
 | RF transmit field map                        | TB1map    | In arbitrary units (arbitrary). Radio frequency (RF) transmit (B1+) field maps are REQUIRED to use this suffix regardless of the method used to generate them. TB1map intensity values are RECOMMENDED to be represented as percent multiplicative factors such that FlipAngle<sub>effective</sub> = B1+<sub>intensity</sub>\*FlipAngle<sub>nominal</sub> .                                                                                                                                                       |
 | RF receive sensitivity map                   | RB1map    | In arbitrary units (arbitrary). Radio frequency (RF) receive (B1-) sensitivity maps are REQUIRED to use this suffix regardless of the method used to generate them. RB1map intensity values are RECOMMENDED to be represented as percent multiplicative factors such that Amplitude<sub>effective</sub> = B1-<sub>intensity</sub>\*Amplitude<sub>ideal</sub>.                                                                                                                                                     |
 | Observed signal amplitude (S0) map           | S0map     | In arbitrary units (arbitrary). For a multi-echo (typically fMRI) sequence, S0 maps index the baseline signal before exponential (T2-star) signal decay. In other words: the exponential of the intercept for a linear decay model across log-transformed echos. For more information, please see, for example, [the tedana documentation](https://tedana.readthedocs.io/en/latest/approach.html#monoexponential-decay-model-fit). S0 maps are RECOMMENDED to use this suffix if derived from an ME-FMRI dataset. |
-| Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (arbitrary). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications (for example, variable flip angle T1 mapping.                                                                                                                                                                                                                                  |
+| Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (arbitrary). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications (for example, variable flip angle T1 mapping).                                                                                                                                                                                                                                  |
 
 Parametric images listed in the table above are typically generated by
 processing a [file collection](../02-common-principles.md#entity-linked-file-collections).

From 2eac22721657cfdb4bf7c9715851a8311302aacb Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 6 Jan 2021 11:47:05 -0500
Subject: [PATCH 77/83] STY: Align table fences

---
 .../01-magnetic-resonance-imaging-data.md                     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 09db9b28d9..8dd38c0d16 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -62,7 +62,7 @@ that a given scan was collected with the intended coil elements selected
 | SpoilingType                | RECOMMENDED if the SpoilingState is `True`.                  | [string][]                             | Specifies which spoiling method(s) are used by a spoiled sequence. Accepted values: `RF`, `GRADIENT` or `COMBINED`.                                                                                                                                                       |
 | SpoilingRFPhaseIncrement    | RECOMMENDED if the SpoilingType is `RF` or `COMBINED`.       | [number][]                             | The amount of incrementation described in degrees, which is applied to the phase of the excitation pulse at each TR period for achieving RF spoiling.                                                                                                                     |
 | SpoilingGradientMoment      | RECOMMENDED if the SpoilingType is `GRADIENT` or `COMBINED`. | [number][]                             | Zeroth moment of the spoiler gradient lobe in millitesla times second per meter (mT.s/m).                                                                                                                                                                                 |
-| SpoilingGradientDuration    | RECOMMENDED if the SpoilingType is `GRADIENT` or `COMBINED`. | [number][]                             | The duration of the spoiler gradient lobe in seconds. The duration of a trapezoidal lobe is defined as the summation of ramp-up and plateau times.                                                                                                                         |
+| SpoilingGradientDuration    | RECOMMENDED if the SpoilingType is `GRADIENT` or `COMBINED`. | [number][]                             | The duration of the spoiler gradient lobe in seconds. The duration of a trapezoidal lobe is defined as the summation of ramp-up and plateau times.                                                                                                                        |
 
 ### In-Plane Spatial Encoding
 | **Key name**                   | **Requirement level** | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
@@ -261,7 +261,7 @@ constitute parametric maps. Currently supported parametric maps include:
 | RF transmit field map                        | TB1map    | In arbitrary units (arbitrary). Radio frequency (RF) transmit (B1+) field maps are REQUIRED to use this suffix regardless of the method used to generate them. TB1map intensity values are RECOMMENDED to be represented as percent multiplicative factors such that FlipAngle<sub>effective</sub> = B1+<sub>intensity</sub>\*FlipAngle<sub>nominal</sub> .                                                                                                                                                       |
 | RF receive sensitivity map                   | RB1map    | In arbitrary units (arbitrary). Radio frequency (RF) receive (B1-) sensitivity maps are REQUIRED to use this suffix regardless of the method used to generate them. RB1map intensity values are RECOMMENDED to be represented as percent multiplicative factors such that Amplitude<sub>effective</sub> = B1-<sub>intensity</sub>\*Amplitude<sub>ideal</sub>.                                                                                                                                                     |
 | Observed signal amplitude (S0) map           | S0map     | In arbitrary units (arbitrary). For a multi-echo (typically fMRI) sequence, S0 maps index the baseline signal before exponential (T2-star) signal decay. In other words: the exponential of the intercept for a linear decay model across log-transformed echos. For more information, please see, for example, [the tedana documentation](https://tedana.readthedocs.io/en/latest/approach.html#monoexponential-decay-model-fit). S0 maps are RECOMMENDED to use this suffix if derived from an ME-FMRI dataset. |
-| Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (arbitrary). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications (for example, variable flip angle T1 mapping).                                                                                                                                                                                                                                  |
+| Equilibrium magnetization (M0) map           | M0map     | In arbitrary units (arbitrary). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications (for example, variable flip angle T1 mapping).                                                                                                                                                                                                                                 |
 
 Parametric images listed in the table above are typically generated by
 processing a [file collection](../02-common-principles.md#entity-linked-file-collections).

From 358370c219876d359e32b1a649fee39cd866cfbe Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Fri, 8 Jan 2021 10:07:57 -0500
Subject: [PATCH 78/83] Move UNIT1 to non-parametric table

---
 .../01-magnetic-resonance-imaging-data.md     | 22 +++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 8dd38c0d16..b4c3e5bfea 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -146,16 +146,17 @@ sub-<label>/[ses-<label>/]
 Anatomical (structural) data acquired for that participant. Currently supported
 non-parametric structural MR images include:
 
-| **Name**                                   | `suffix`         | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
-| ------------------------------------------ | ---------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| T1 weighted images                         | T1w              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the longitudinal relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively short repetition and echo times. To achieve this weighting in gradient-echo images, again, short repetition and echo times are selected; however, at relatively large flip angles. Another common approach to increase T1 weighting in gradient-echo images is to add an inversion preparation block to the beginning of the imaging sequence (for example, `TurboFLASH` or `MP-RAGE`). |
-| T2 weighted images                         | T2w              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the (true) transverse relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively long repetition and echo times. Generally, gradient echo sequences are not the most suitable option for achieving T2 weighting, as their contrast natively depends on T2-star rather than on T2.                                                                                                                                                                                   |
-| Proton density (PD) weighted images        | PDw              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the spin density (1H) of the imaged specimen. In spin-echo sequences this contrast is achieved at short repetition and long echo times. In a gradient-echo acquisition, PD weighting dominates the contrast at long repetition and short echo times, and at small flip angles.                                                                                                                                                                                                                                  |
-| T2star weighted images                     | T2starw          | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the (observed) transverse relaxation time of the imaged specimen. In spin-echo sequences, this effect is negated as the excitation is followed by an inversion pulse. The contrast of gradient-echo images natively depends on T2-star effects. However, for T2-star variation to dominate the image contrast, gradient-echo acquisitions are carried out at long repetition and echo times, and at small flip angles.                                                                                          |
-| Fluid attenuated inversion recovery images | FLAIR            | In arbitrary units (arbitrary). Structural images with predominant T2 contribution (a.k.a T2-FLAIR), in which signal from fluids (for example, CSF) is nulled out by adjusting inversion time, coupled with notably long repetition and echo times.                                                                                                                                                                                                                                                                                                                                                                        |
-| Inplane T1                                 | inplaneT1        | In arbitrary units (arbitrary). T1 weighted structural image matched to a functional (task) image.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
-| Inplane T2                                 | inplaneT2        | In arbitrary units (arbitrary). T2 weighted structural image matched to a functional (task) image.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
-| PD and T2 weighted images                  | PDT2             | In arbitrary units (arbitrary). PDw and T2w images acquired using a dual echo FSE sequence through view sharing process ([Johnson et al. 1994](https://pubmed.ncbi.nlm.nih.gov/8010268/)).                                                                                                                                                                                                                                                                                                                                                                                                                                 |
+| **Name**                                     | `suffix`         | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
+| -------------------------------------------- | ---------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| T1 weighted images                           | T1w              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the longitudinal relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively short repetition and echo times. To achieve this weighting in gradient-echo images, again, short repetition and echo times are selected; however, at relatively large flip angles. Another common approach to increase T1 weighting in gradient-echo images is to add an inversion preparation block to the beginning of the imaging sequence (for example, `TurboFLASH` or `MP-RAGE`). |
+| T2 weighted images                           | T2w              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the (true) transverse relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively long repetition and echo times. Generally, gradient echo sequences are not the most suitable option for achieving T2 weighting, as their contrast natively depends on T2-star rather than on T2.                                                                                                                                                                                   |
+| Proton density (PD) weighted images          | PDw              | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the spin density (1H) of the imaged specimen. In spin-echo sequences this contrast is achieved at short repetition and long echo times. In a gradient-echo acquisition, PD weighting dominates the contrast at long repetition and short echo times, and at small flip angles.                                                                                                                                                                                                                                  |
+| T2star weighted images                       | T2starw          | In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the (observed) transverse relaxation time of the imaged specimen. In spin-echo sequences, this effect is negated as the excitation is followed by an inversion pulse. The contrast of gradient-echo images natively depends on T2-star effects. However, for T2-star variation to dominate the image contrast, gradient-echo acquisitions are carried out at long repetition and echo times, and at small flip angles.                                                                                          |
+| Fluid attenuated inversion recovery images   | FLAIR            | In arbitrary units (arbitrary). Structural images with predominant T2 contribution (a.k.a T2-FLAIR), in which signal from fluids (for example, CSF) is nulled out by adjusting inversion time, coupled with notably long repetition and echo times.                                                                                                                                                                                                                                                                                                                                                                        |
+| Inplane T1                                   | inplaneT1        | In arbitrary units (arbitrary). T1 weighted structural image matched to a functional (task) image.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
+| Inplane T2                                   | inplaneT2        | In arbitrary units (arbitrary). T2 weighted structural image matched to a functional (task) image.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
+| PD and T2 weighted images                    | PDT2             | In arbitrary units (arbitrary). PDw and T2w images acquired using a dual echo FSE sequence through view sharing process ([Johnson et al. 1994](https://pubmed.ncbi.nlm.nih.gov/8010268/)).                                                                                                                                                                                                                                                                                                                                                                                                                                 |
+| Homogeneous (flat) T1-weighted MP2RAGE image | UNIT1            | In arbitrary units (arbitrary). UNIT1 images are REQUIRED to use this suffix regardless of the method used to generate them. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from from `T1w`. Plase see [`MP2RAGE` specific notes](../99-appendices/11-qmri.md#unit1-images) in the qMRI appendix for further information.                                   |
 
 If the structural images included in the dataset were defaced (to protect
 identity of participants) one MAY provide the binary mask that was used to
@@ -252,7 +253,6 @@ constitute parametric maps. Currently supported parametric maps include:
 | Proton density map                           | PDmap     | In arbitrary units (arbitrary). PD maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                           |
 | Magnetization transfer ratio map             | MTRmap    | In arbitrary units (arbitrary). MTR maps are REQUIRED to use this suffix regardless of the method used to generate them. MTRmap intensity values are RECOMMENDED to be represented in percentage in the range of 0-100%.                                                                                                                                                                                                                                                                                          |
 | Magnetization transfer saturation map        | MTsat     | In arbitrary units (arbitrary). MTsat maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                        |
-| Homogeneous (flat) T1-weighted MP2RAGE image | UNIT1     | In arbitrary units (arbitrary). UNIT1 images are REQUIRED to use this suffix regardless of the method used to generate them. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from from `T1w`.                                                                                                                                                        |
 | T1 in rotating frame (T1 rho) map            | T1rho     | In seconds (s). T1-rho maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                                       |
 | Myelin water fraction map                    | MWFmap    | In arbitrary units (arbitrary). MWF maps are REQUIRED to use this suffix regardless of the method used to generate them. MWF intensity values are RECOMMENDED to be represented in percentage in the range of 0-100%.                                                                                                                                                                                                                                                                                             |
 | Macromolecular tissue volume (MTV) map       | MTVmap    | In arbitrary units (arbitrary). MTV maps are REQUIRED to use this suffix regardless of the method used to generate them.                                                                                                                                                                                                                                                                                                                                                                                          |

From 8a327a9619b93351ac2523ea73b2fd5822c39fba Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Fri, 8 Jan 2021 10:27:26 -0500
Subject: [PATCH 79/83] Fix typo

---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index bc6724151f..b7a2f23c48 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -144,7 +144,7 @@ Explanation of the table:
 -   The metadata fields listed in the REQUIRED column are needed to perform a minimum viable qMRI processing for the corresponding `file collection`.
 
 -   Note that some of the metadata fields may be constant across different files in a file collection,
-    yet still required as an input (for example, `NumberShots` in `MP2AGE`).
+    yet still required as an input (for example, `NumberShots` in `MP2RAGE`).
     Such metadata fields MUST be provided in the accompanying JSON files.
 
 -   The metadata fields listed in the OPTIONAL column can be used to form different flavors of an existing file collection suffix,

From 43edcabbd0526704d034a69cea63e7091faa1930 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Fri, 8 Jan 2021 10:28:10 -0500
Subject: [PATCH 80/83] Fix typo

---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index b7a2f23c48..7e0b9f743c 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -166,7 +166,7 @@ Explanation of the table:
 
 <sup>*</sup> Please see TB1SRGE-specific notes for the calculation of `NumberShots`.
 
-### Meta-data requirements for qMRI maps
+### Metadata requirements for qMRI maps
 
 As qMRI maps are stored as derivatives, they are subjected to the metadata requirements of
 [derived datasets](../03-modality-agnostic-files.md#derived-dataset-and-pipeline-description).

From 0776ebf5b356b0527eb2624f9a9dcc7f8a78dc93 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Fri, 8 Jan 2021 10:31:47 -0500
Subject: [PATCH 81/83] Drop the term grayscale

---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 7e0b9f743c..c83013b409 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -3,7 +3,7 @@
 Quantitative MRI (qMRI) is a collection of methods aiming at generating parametric maps
 that can characterize underlying tissue properties.
 Unlike those of conventional MR images (for example, `T1w` or `T2w`),
-intensity values of quantitative maps are not represented in an arbitrary grayscale range.
+intensity values of quantitative maps are not represented in an arbitrary range.
 Instead, these maps are represented either in absolute physical units
 (for example, `seconds` for `T1map`),
 or within an application dependent range of arbitrary units

From 2a9cb0c4ca51b11bd40fc761e4797eff2c6d8ec2 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Fri, 8 Jan 2021 10:56:12 -0500
Subject: [PATCH 82/83] Align table fence

---
 .../01-magnetic-resonance-imaging-data.md                       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index b4c3e5bfea..32f66c95d1 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -156,7 +156,7 @@ non-parametric structural MR images include:
 | Inplane T1                                   | inplaneT1        | In arbitrary units (arbitrary). T1 weighted structural image matched to a functional (task) image.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
 | Inplane T2                                   | inplaneT2        | In arbitrary units (arbitrary). T2 weighted structural image matched to a functional (task) image.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
 | PD and T2 weighted images                    | PDT2             | In arbitrary units (arbitrary). PDw and T2w images acquired using a dual echo FSE sequence through view sharing process ([Johnson et al. 1994](https://pubmed.ncbi.nlm.nih.gov/8010268/)).                                                                                                                                                                                                                                                                                                                                                                                                                                 |
-| Homogeneous (flat) T1-weighted MP2RAGE image | UNIT1            | In arbitrary units (arbitrary). UNIT1 images are REQUIRED to use this suffix regardless of the method used to generate them. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from from `T1w`. Plase see [`MP2RAGE` specific notes](../99-appendices/11-qmri.md#unit1-images) in the qMRI appendix for further information.                                   |
+| Homogeneous (flat) T1-weighted MP2RAGE image | UNIT1            | In arbitrary units (arbitrary). UNIT1 images are REQUIRED to use this suffix regardless of the method used to generate them. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from from `T1w`. Plase see [`MP2RAGE` specific notes](../99-appendices/11-qmri.md#unit1-images) in the qMRI appendix for further information.                                                                                                                                                                                                                                                                                                                                                                                                                      |
 
 If the structural images included in the dataset were defaced (to protect
 identity of participants) one MAY provide the binary mask that was used to

From 30e69300ff9ab157f537179d5e993302053335a5 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Fri, 8 Jan 2021 12:44:28 -0500
Subject: [PATCH 83/83] STY: Align table fences

---
 .../01-magnetic-resonance-imaging-data.md                       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 32f66c95d1..f876857dd4 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -156,7 +156,7 @@ non-parametric structural MR images include:
 | Inplane T1                                   | inplaneT1        | In arbitrary units (arbitrary). T1 weighted structural image matched to a functional (task) image.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
 | Inplane T2                                   | inplaneT2        | In arbitrary units (arbitrary). T2 weighted structural image matched to a functional (task) image.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
 | PD and T2 weighted images                    | PDT2             | In arbitrary units (arbitrary). PDw and T2w images acquired using a dual echo FSE sequence through view sharing process ([Johnson et al. 1994](https://pubmed.ncbi.nlm.nih.gov/8010268/)).                                                                                                                                                                                                                                                                                                                                                                                                                                 |
-| Homogeneous (flat) T1-weighted MP2RAGE image | UNIT1            | In arbitrary units (arbitrary). UNIT1 images are REQUIRED to use this suffix regardless of the method used to generate them. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from from `T1w`. Plase see [`MP2RAGE` specific notes](../99-appendices/11-qmri.md#unit1-images) in the qMRI appendix for further information.                                                                                                                                                                                                                                                                                                                                                                                                                      |
+| Homogeneous (flat) T1-weighted MP2RAGE image | UNIT1            | In arbitrary units (arbitrary). UNIT1 images are REQUIRED to use this suffix regardless of the method used to generate them. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from from `T1w`. Plase see [`MP2RAGE` specific notes](../99-appendices/11-qmri.md#unit1-images) in the qMRI appendix for further information.                                                                                                                                    |
 
 If the structural images included in the dataset were defaced (to protect
 identity of participants) one MAY provide the binary mask that was used to