From 407a31ad9682ed2dfb21a7ddf4fd9b6b5b7a06b3 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 22 Apr 2020 05:15:32 -0400
Subject: [PATCH 01/76] [CHANGE] modality_label --> suffix

* Suffix has a wider semantic scope than "modality"
* So that it can better represent different types of anatomy imaging applications
---
 .../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 5e652f866b..12a6aa16a7 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
@@ -113,8 +113,8 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     anat/
-        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_<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>][_part-<mag/phase>][_ce-<label>][_rec-<label>][_run-<index>]_<suffix>.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<suffix>]_defacemask.nii[.gz]
 ```
 
 Anatomical (structural) data acquired for that participant. Currently supported

From 1620c36537e57d9f8342498edee73fcfb87cb2fa Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 22 Apr 2020 05:28:06 -0400
Subject: [PATCH 02/76] [REMOVE] Modality table

* The removed table was an incoherent collection of MRI terms, in which sequence names (e.g. FLASH), weighting labels (e.g. T1w), parametric maps (e.g. T1map) and unspecified MR attributes (e.g. PD) were collapsed under the term "modality".
* Format specified by a sequence name does not necessarily ensure interchangeability, given that the same sequence can generate different contrasts.
* Descriptions were missing for 8/14 entries.
* Existing descriptions were not comprehensive.
---
 .../01-magnetic-resonance-imaging-data.md     | 20 -------------------
 1 file changed, 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 12a6aa16a7..16dcacc534 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
@@ -117,26 +117,6 @@ sub-<label>/[ses-<label>/]
         sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_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            |                                                                                                                                                   |
-
 #### The `run` entity
 
 If several scans of the same modality are acquired they MUST be indexed with a

From c9d91e9fe94d1c0acc861853e19f269306101c59 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 22 Apr 2020 05:29:48 -0400
Subject: [PATCH 03/76] [ADD] Introductory text

* A brief description, expanding on the scope of anatomy imaging using MRI
---
 .../01-magnetic-resonance-imaging-data.md              | 10 ++++++++++
 1 file changed, 10 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 16dcacc534..f688b5ff16 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
@@ -117,6 +117,16 @@ sub-<label>/[ses-<label>/]
         sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<suffix>]_defacemask.nii[.gz]
 ```
 
+The term anatomical imaging data spans a broad range of MRI applications. These
+applications share in common the ability to convey structural information about
+the imaged anatomy, but differ by the nature of the data they contain. Anatomical
+(structural) data for a participant may refer to:
+* a single standalone data set (e.g. a 3D high resolution T1-weighted image)
+* a group of images acquired for the purpose of improving contrast characteristics 
+or calculating quantitative maps
+(e.g. four 3D volumes provided as an input to an MP2RAGE calculation) 
+* the quantitative maps themselves (e.g. `T1map` etc.).
+
 #### The `run` entity
 
 If several scans of the same modality are acquired they MUST be indexed with a

From 75951628fdc5cac27483eb1569bb3ce63c84b420 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 22 Apr 2020 05:33:19 -0400
Subject: [PATCH 04/76] [ADD] Description abt conventional acq

* Added as a subsection to the Anatomy imaging data section.
---
 .../01-magnetic-resonance-imaging-data.md          | 14 ++++++++++++++
 1 file changed, 14 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 f688b5ff16..5fd9253ef1 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
@@ -127,6 +127,20 @@ or calculating quantitative maps
 (e.g. four 3D volumes provided as an input to an MP2RAGE calculation) 
 * the quantitative maps themselves (e.g. `T1map` etc.).
 
+#### Conventional structural acquisitions
+
+Anatomical images of this type typically refer to a volumetric high-resolution 
+dataset, representing the measured MRI signal in an arbitrary scale of gray
+shades. Contrast factor of these grayscale images depend on the relative contribution
+of inherent tissue parameters (e.g. `T1`, `T2` and `PD`) to the measured signal. 
+
+Contribution weights of these parameters are determined by the type of acquisition
+sequence (e.g. `spin-` or `gradient-echo`) and the setting of various parameters
+(e.g. `Repetition Time`, `Echo Time`, `Inversion Time` and `Flip Angle`). For 
+example, in a spoiled gradient-echo scan, keeping the repetition and the echo time 
+short with a relatively large flip angle increases the contribution of `T1`, yielding
+a primarily T1-weighted image.
+
 #### The `run` entity
 
 If several scans of the same modality are acquired they MUST be indexed with a

From f2138caa5749dfd77c06c9d1d365b95c41bc3913 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 22 Apr 2020 05:37:29 -0400
Subject: [PATCH 05/76] [ADD] Description abt grouped scans

* Why a bundle of images may be needed.
* Introduce the term `grouped scan collections`
* Why suffix is made adaptive to the type of anatomy imaging method.
---
 .../01-magnetic-resonance-imaging-data.md     | 19 +++++++++++++++++++
 1 file changed, 19 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 5fd9253ef1..cb9f4cac13 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
@@ -141,6 +141,25 @@ example, in a spoiled gradient-echo scan, keeping the repetition and the echo ti
 short with a relatively large flip angle increases the contribution of `T1`, yielding
 a primarily T1-weighted image.
 
+#### Grouped scan collections for contrast improvement or quantitative map calculation
+
+A group of anatomical scans may be collected to enhance certain contrast features,
+such as to calculate a weighted average of multi-echo gradient echo (`MEGRE`) images,
+which is known to improve segmentation algorithm outputs. Note that outputs from
+this approach are still in the confines of an arbitrary grayscale representation.
+
+Quantitative MRI (qMRI) methods mathematically characterize the signal changes observed in a collection of parametrically altered scans under certain biophysical model assumptions. These `grouped scan collections` are then processed to derive a `qMRI map`, representing anatomical features in a physically meaningful parameter range.
+
+In both cases, the contrast characteristics change with varying acquisition parameters across `grouped scan collections`. Therefore, it is not tenable to name all the members
+of a `grouped scan collection` with one conventional MRI suffix label (e.g., `T1w`)
+or any other label that implies interchangeability among its instances. 
+
+To circumvent this problem, the `_<suffix>` entity is adaptively used according 
+to the intended application of anatomical imaging data. For conventional MRI 
+applications, the suffixes will correspond to common anatomical contrasts `T1w`,
+`T2w`, `T2starw` etc. For groups of scans acquired for contrast improvement or 
+qMRI processing, the `_<suffix>` indicates the collection that the scans belong to.
+
 #### The `run` entity
 
 If several scans of the same modality are acquired they MUST be indexed with a

From b5b655e1321e775b0e7808fd9694da4f9eea47ff Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 22 Apr 2020 07:27:10 -0400
Subject: [PATCH 06/76] [ADD] Suffix entity subsection

* Suffix is divided into 3 categories for:
     * Conventional MRI
     * Grouped scans
     * qMRI maps
* Add note about legacy suffixes
---
 .../01-magnetic-resonance-imaging-data.md        | 16 ++++++++++++++++
 1 file changed, 16 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 5e652f866b..63f899d371 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
@@ -136,6 +136,22 @@ modalities include:
 | Inplane T1         | inplaneT1        | T1-weighted anatomical image matched to functional acquisition                                                                                    |
 | Inplane T2         | inplaneT2        | T2-weighted anatomical image matched to functional acquisition                                                                                    |
 | Angiography        | angio            |                                                                                                                                                   |
+#### The `_<suffix>` entity
+
+To ensure an comprehensible, human readable directory that contains anatomical 
+imaging data, the `_<suffix>` entity can be used in one of three ways:
+
+1. Conventional MRI suffixes
+2. Grouping suffixes
+3. Quantitative MRI (qMRI) map suffixes
+
+This distinction was added to the specification on acceptance of the BEP001 
+proposal in version `1.x.x`. As a result there are some additional suffixes that
+are no longer recommended but remain part of the specification in order to 
+maintain backwards compatability with previous versions of the specification.
+These can be found in the [legacy suffixes](#legacy-suffixes) subsection.
+
+Previous versions of the specification used the term `modality_label` instead of `_suffix` to represent this entity. The change in term was introduced in version 1.x.x. to accodomate a broad definition of anatomical imaging applications.
 
 #### The `run` entity
 

From 31004736856218245f1288d0c6ea09f253b7b2fe Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 22 Apr 2020 07:28:47 -0400
Subject: [PATCH 07/76] [ADD] Legacy suffixes table

* For existing datasets
---
 .../01-magnetic-resonance-imaging-data.md            | 12 ++++++++++++
 1 file changed, 12 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 63f899d371..f2a57df363 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
@@ -204,6 +204,18 @@ fields specific to anatomical scans:
 | -----------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------- |
 | ContrastBolusIngredient | OPTIONAL. Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048. |
 
+##### Legacy suffixes (to be deprecated)
+
+Some suffixes that were available in versions of the specification prior to 1.x.x. have been identified as legacy suffixes. The legacy sufficies generate inconsistencies and/or ambiguities with additional sufficies added in version 1.x.x and so are therefore not recommended for use in new datasets. They remain valid sufficies to maintain backwards compatibility with earlier datasets.

+
+The following suffixes are valid, but SHOULD NOT be used for new BIDS compatible datasets (created after version 1.x.x.):
+
+| Name           | Suffix    | Description                                                    | Reason to deprecate                                                                                                                                                                                                                                                                                                                                                                                                |
+|----------------|-----------|----------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| T2\*           | T2star    | Not provided.                                                  | Ambiguous, may refer to a parametric image or to a conventional image. **Change:** Replaced by `T2starw` or `T2starmap`.                                                                                                                                                                                                                                                                                           |
+| FLASH          | FLASH     | Not provided.                                                  | 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. Given the versatility and the popularity of the FLASH sequence, it can easily obfuscate purpose of a  `grouped scan collection` when used as a `grouping suffix`. **Change:** Removed from suffixes.     |
+| Proton Density | PD        | Not provided.                                                  | 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 3aeb1ce433ca25e7584cee8e856886ca4e3b2439 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 22 Apr 2020 08:03:50 -0400
Subject: [PATCH 08/76] [ADD] Grouping suffix

* Function description
---
 .../01-magnetic-resonance-imaging-data.md                  | 7 +++++++
 1 file changed, 7 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 5e652f866b..f967808924 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
@@ -136,6 +136,13 @@ modalities include:
 | Inplane T1         | inplaneT1        | T1-weighted anatomical image matched to functional acquisition                                                                                    |
 | Inplane T2         | inplaneT2        | T2-weighted anatomical image matched to functional acquisition                                                                                    |
 | Angiography        | angio            |                                                                                                                                                   |
+##### Grouping suffixes
+
+**Function:**
+
+Files that belong to a **grouped scan collection** are intended to be used together within a qMRI analysis framework.
+The quantitative maps that are output from these calculations (e.g., `T1map`, `T2map` etc) are described in the [qMRI map suffixes](#qmri-map-suffixes) section below.
+A change to the specification is REQUIRED to expand or to modify the following table.
 
 #### The `run` entity
 

From 984574d503bc180f3d442ab1ec160694b389f6c0 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 22 Apr 2020 08:05:29 -0400
Subject: [PATCH 09/76] [ADD] Table for grouping suffix

* VFA, IRT1, MP2RAGE, MESE, MEGRE, MTR, MTS, MPM, B1DAM
---
 .../01-magnetic-resonance-imaging-data.md            | 12 ++++++++++++
 1 file changed, 12 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 f967808924..51f1de150a 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
@@ -144,6 +144,18 @@ Files that belong to a **grouped scan collection** are intended to be used toget
 The quantitative maps that are output from these calculations (e.g., `T1map`, `T2map` etc) are described in the [qMRI map suffixes](#qmri-map-suffixes) section below.
 A change to the specification is REQUIRED to expand or to modify the following table.
 
+| Name                                       | Suffix  | Type     | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
+|--------------------------------------------|---------|----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| Variable flip angle                        | VFA     | Grouping | Parametrically linked anatomical images (primarily) for relaxometry mapping. 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. Please visit the [qMRI appendix](#prioritylevels) for details. _Associated output suffixes_: T1map, T2map, R1map, R2map |
+| Inversion recovery (for T1 mapping)        | IRT1    | Grouping | Parametrically linked anatomical images for T1 mapping. The IRT1 method involves multiple inversion recovery spin-echo images acquired at different inversion times. _Associated output suffixes_: T1map, R1map                                                                                                                                                                                                                                                                                                                    |
+| Magnetization prepared two gradient echoes | MP2RAGE | Grouping | Parametrically linked anatomical images (primarily) for T1 mapping. 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. _Associated output suffixes_: T1map, R1map, UNIT1                                                                                                                                                                                                                 |
+| Multi-echo spin echo                       | MESE    | Grouping | Parametrically linked anatomical images (primarily) for T2 mapping.The MESE method involves multiple spin echo images acquired at different echo times. _Associated output suffixes_: T2map, R2map, MWFmap                                                                                                                                                                                                                                                                                                                         |
+| Multi-echo gradient echo                   | MEGRE   | Grouping | Parametrically linked multiple anatomical gradient echo images acquired at different echo times. _Associated output suffixes_: T2starmap, R2starmap, when used for T2* mapping.                                                                                                                                                                                                                                                                                                                                                    |
+| Magnetization transfer ratio               | MTR     | Grouping | Parametrically linked anatomical images for calculating a semi-quantitative magnetization transfer ratio map. _Associated output suffixes_: MTRmap                                                                                                                                                                                                                                                                                                                                                                                 |
+| Magnetization transfer saturation          | MTS     | Grouping | Parametrically linked anatomical images for calculating 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. _Associated output suffixes_: T1map, MTsat                                                                                                                                                                                               |
+| Multi-parametric mapping                   | MPM     | Grouping | Parametrically linked anatomical images for multiparametric mapping (a.k.a hMRI). The MPM method involves anatomical images differing in terms of application of a magnetization transfer RF pulse (MTon or MToff), flip angle and (optionally) echo time and magnitue/phase parts. Please visit [here](https://owncloud.gwdg.de/index.php/s/iv2TOQwGy4FGDDZ) for suggested MPM acquisition protocols.,_Associated output suffixes_:R1map, R2starmap, MTsat, PDmap, T1map, T2starmap                                               |
+| Double-angle B1 mapping                    | B1DAM   | Grouping | Parametrically linked anatomical images for RF transmit field (B1 plus) mapping. Double angle method is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation angles. Common sequence types for this application include spin echo and echo planar imaging. _Associated output suffixes_: B1plusmap                                                                                                                                                      |
+
 #### The `run` entity
 
 If several scans of the same modality are acquired they MUST be indexed with a

From f79b2a5da66fa979e82720ff00989cf752045712 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 22 Apr 2020 08:06:55 -0400
Subject: [PATCH 10/76] [ADD] Example snippet and note

* Reference to the entity table and qMRI appendix
* Note regarding the use of constituent images of a grouping suffix for structural data processing.
---
 .../01-magnetic-resonance-imaging-data.md     | 20 +++++++++++++++++++
 1 file changed, 20 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 51f1de150a..09e86bac41 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
@@ -155,6 +155,26 @@ A change to the specification is REQUIRED to expand or to modify the following t
 | Magnetization transfer saturation          | MTS     | Grouping | Parametrically linked anatomical images for calculating 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. _Associated output suffixes_: T1map, MTsat                                                                                                                                                                                               |
 | Multi-parametric mapping                   | MPM     | Grouping | Parametrically linked anatomical images for multiparametric mapping (a.k.a hMRI). The MPM method involves anatomical images differing in terms of application of a magnetization transfer RF pulse (MTon or MToff), flip angle and (optionally) echo time and magnitue/phase parts. Please visit [here](https://owncloud.gwdg.de/index.php/s/iv2TOQwGy4FGDDZ) for suggested MPM acquisition protocols.,_Associated output suffixes_:R1map, R2starmap, MTsat, PDmap, T1map, T2starmap                                               |
 | Double-angle B1 mapping                    | B1DAM   | Grouping | Parametrically linked anatomical images for RF transmit field (B1 plus) mapping. Double angle method is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation angles. Common sequence types for this application include spin echo and echo planar imaging. _Associated output suffixes_: B1plusmap                                                                                                                                                      |
+For example:
+
+```Text
+sub-01_fa-1_VFA.nii.gz
+sub-01_fa-1_VFA.json
+sub-01_fa-2_VFA.nii.gz
+sub-01_fa-2_VFA.json
+```
+
+Please see the [entity table appendix]() for the REQUIRED and OPTIONAL entities
+for each `grouping suffix`. 
+
+Note that every image in a **grouped scan collection** has the same `_<suffix>` 
+as they are likely to be used together.
+Although the acquisitions will have many identical acquisition parameters, only one-to-one-mapping is allowed between a `.json`-sidecar file and an image in a 
+grouped scan collection. This means that parameter values that are identical 
+across a set of grouped scans will still have to be stored separately in each `.json`-sidecar file.
+
+Note: Individual images within a grouped scan collection may be used for any purpose.
+For example, the acquisition that is most similar to a `T1w` image may be used in analysis pipelines needing a conventional T1-weighted image.
 
 #### The `run` entity
 

From 5b671b12b72f316fef88b4a693a66d6d485fb326 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 22 Apr 2020 08:37:12 -0400
Subject: [PATCH 11/76] [ADD] qMRI map suffix

* Function description
---
 .../01-magnetic-resonance-imaging-data.md                | 9 +++++++++
 1 file changed, 9 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 5e652f866b..dcf7c9dd83 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
@@ -136,6 +136,15 @@ modalities include:
 | Inplane T1         | inplaneT1        | T1-weighted anatomical image matched to functional acquisition                                                                                    |
 | Inplane T2         | inplaneT2        | T2-weighted anatomical image matched to functional acquisition                                                                                    |
 | Angiography        | angio            |                                                                                                                                                   |
+#### qMRI map suffixes
+
+**Function:**
+
+Denotes the parameter contained within an individual file of a
+quantitative parametric image.
+
+Changes to the specification is REQUIRED to
+expand or to modify the following table.
 
 #### The `run` entity
 

From 7cc7dc9a803034a1f1a88339790f7a4f2e862fc7 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 22 Apr 2020 08:45:01 -0400
Subject: [PATCH 12/76] [ADD] Table for qMRI

* T1map, T2map, T2starmap, R1map, R2map, R2starmap, PDmap, MTRmap, MTsat, UNIT1, T1rho, MWFmap, PDT2map, B1plusmap
---
 .../01-magnetic-resonance-imaging-data.md       | 17 +++++++++++++++++
 1 file changed, 17 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 dcf7c9dd83..2a5217dda8 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
@@ -146,6 +146,23 @@ quantitative parametric image.
 Changes to the specification is REQUIRED to
 expand or to modify the following table.
 
+| Name                                                   | _suffix   | _suffix type | Description                                                                                                                                                                                                                                                                          |
+|--------------------------------------------------------|-----------|--------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| Longitudinal relaxation time map                       | T1map     | Parametric   | In seconds (s). T1 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `VFA`, `IRT1`, `MP2RAGE`, `MTS`,`MPM`. You can visit [this interactive book for T1 mapping](https://qmrlab.org/t1_book/intro) for further reading.  |
+| True transverse relaxation time map                    | T2map     | Parametric   | In seconds (s). T2 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`, `MPM`                                                                                                                                       |
+| Observed transverse relaxation time map                | T2starmap | Parametric   | In seconds (s). T2* maps are REQUIRED to use this suffix irrespective of the method they are related to._Can be generated from:_ `MEGRE`, `MPM`                                                                                                                                      |
+| Longitudinal relaxation rate map                       | R1map     | Parametric   | In seconds-1 (1/s). R1 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `VFA`, `IRT1`, `MP2RAGE`, `MTS`, `MPM`                                                                                                           |
+| True transverse relaxation rate map                    | R2map     | Parametric   | In seconds-1 (1/s). R2 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`, `MPM`                                                                                                                                  |
+| Observed transverse relaxation rate map                | R2starmap | Parametric   | In seconds-1 (1/s). R2* maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_`MEGRE`, `MPM`                                                                                                                                 |
+| Proton density map                                     | PDmap     | Parametric   | In arbitrary units (a.u.). PD maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MPM`                                                                                                                                    |
+| Magnetization transfer ratio map                       | MTRmap    | Parametric   | In percentage (%). MTR maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MTR`                                                                                                                                           |
+| Magnetization transfer saturation index map            | MTSat     | Parametric   | In arbitrary units (a.u.). MTsat maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MTS`, `MPM`                                                                                                                          |
+| Homogeneous (flat) T1 image by MP2RAGE                 | UNIT1     | Parametric   | In arbitrary units (a.u.). UNIT1 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MP2RAGE`                                                                                                                             |
+| Longutidunal relaxation in rotating frame (T1 rho) map | T1rho     | Parametric   | In seconds (s). T1-rho maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ N/A                                                                                                                                             |
+| Myelin water fraction map                              | MWFmap    | Parametric   | In percentage (%). MWF maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`                                                                                                                                          |
+| Combined PD/T2 map                                     | PDT2map   | Parametric   | In arbitrary units (a.u.). Combined PD/T2 maps are REQUIRED to use this suffix irrespective of the method they are related to. N/A                                                                                                                                                   |
+| RF transmit field map                                  | B1plusmap | Parametric   | In arbitrary units (a.u.). Radio frequency (RF) transmit field maps are REQUIRED to use this suffix irrespective of the method they are related to. For further details please see the fieldmap data section.  _Can be generated from_: `B1DAM`                                                                      |
+
 #### The `run` entity
 
 If several scans of the same modality are acquired they MUST be indexed with a

From 63cd04922f206339e9ee0fd6a471e81c58760f58 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 22 Apr 2020 08:45:50 -0400
Subject: [PATCH 13/76] [ADD] Example snippet and note

---
 .../01-magnetic-resonance-imaging-data.md      | 18 +++++++++++++++++-
 1 file changed, 17 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 2a5217dda8..ed2e1b571d 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
@@ -156,13 +156,29 @@ expand or to modify the following table.
 | Observed transverse relaxation rate map                | R2starmap | Parametric   | In seconds-1 (1/s). R2* maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_`MEGRE`, `MPM`                                                                                                                                 |
 | Proton density map                                     | PDmap     | Parametric   | In arbitrary units (a.u.). PD maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MPM`                                                                                                                                    |
 | Magnetization transfer ratio map                       | MTRmap    | Parametric   | In percentage (%). MTR maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MTR`                                                                                                                                           |
-| Magnetization transfer saturation index map            | MTSat     | Parametric   | In arbitrary units (a.u.). MTsat maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MTS`, `MPM`                                                                                                                          |
+| Magnetization transfer saturation index map            | MTsat     | Parametric   | In arbitrary units (a.u.). MTsat maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MTS`, `MPM`                                                                                                                          |
 | Homogeneous (flat) T1 image by MP2RAGE                 | UNIT1     | Parametric   | In arbitrary units (a.u.). UNIT1 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MP2RAGE`                                                                                                                             |
 | Longutidunal relaxation in rotating frame (T1 rho) map | T1rho     | Parametric   | In seconds (s). T1-rho maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ N/A                                                                                                                                             |
 | Myelin water fraction map                              | MWFmap    | Parametric   | In percentage (%). MWF maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`                                                                                                                                          |
 | Combined PD/T2 map                                     | PDT2map   | Parametric   | In arbitrary units (a.u.). Combined PD/T2 maps are REQUIRED to use this suffix irrespective of the method they are related to. N/A                                                                                                                                                   |
 | RF transmit field map                                  | B1plusmap | Parametric   | In arbitrary units (a.u.). Radio frequency (RF) transmit field maps are REQUIRED to use this suffix irrespective of the method they are related to. For further details please see the fieldmap data section.  _Can be generated from_: `B1DAM`                                                                      |
 
+Quantitative maps can be obtained right off the scanner or by processing files
+belonging to a `grouped scan collection`. Regardless of the method they are
+obtained by, one of the `_suffix` entries listed in the table above is REQUIRED
+for a proper naming. For example:
+
+```Text
+sub-01_T1map.nii.gz
+sub-01_T1map.json
+```
+**Important:**
+
+Quantitative unit of the parameter contained by a quantitative map MUST comply
+with the unit description provided for its respective `_suffix` entry.
+For example, a T1 map in milliseconds unit (ms) is not valid, given that the
+description of the `T1map` suffix requires the parameter to be in seconds (s).
+
 #### The `run` entity
 
 If several scans of the same modality are acquired they MUST be indexed with a

From 82616ecd23f3e7174c99d8cdc13f1d472e2de74b Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Fri, 24 Apr 2020 09:42:42 +0200
Subject: [PATCH 14/76] Some small textual changes

---
 .../01-magnetic-resonance-imaging-data.md     | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 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 cb9f4cac13..68323a784c 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
@@ -117,15 +117,16 @@ sub-<label>/[ses-<label>/]
         sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<suffix>]_defacemask.nii[.gz]
 ```
 
-The term anatomical imaging data spans a broad range of MRI applications. These
-applications share in common the ability to convey structural information about
-the imaged anatomy, but differ by the nature of the data they contain. Anatomical
-(structural) data for a participant may refer to:
-* a single standalone data set (e.g. a 3D high resolution T1-weighted image)
-* a group of images acquired for the purpose of improving contrast characteristics 
-or calculating quantitative maps
+The term anatomical imaging data pertains to a broad range of MRI applications that provide structural 
+information about (brain) anatomy, but differ by the nature of the data they contain. Anatomical
+(structural) data for a participant may refer to three types of data:
+1. a single image with specific weighting on an arbitrary scale (e.g. a 3D high resolution T1-weighted image).
+This type is most commonly used in neuroimaging applications.
+2. a group of images acquired within a single protocol for the purpose of improving contrast 
+characteristics (e.g., a multi-echo anatomical GRE image) or calculating quantitative maps
 (e.g. four 3D volumes provided as an input to an MP2RAGE calculation) 
-* the quantitative maps themselves (e.g. `T1map` etc.).
+3. a quantitative map of which the intensities are put on an absolute scales (e.g., seconds for a T1 map).
+These images are generally produced by some mathematical operation on images from class 2.
 
 #### Conventional structural acquisitions
 
@@ -145,8 +146,7 @@ a primarily T1-weighted image.
 
 A group of anatomical scans may be collected to enhance certain contrast features,
 such as to calculate a weighted average of multi-echo gradient echo (`MEGRE`) images,
-which is known to improve segmentation algorithm outputs. Note that outputs from
-this approach are still in the confines of an arbitrary grayscale representation.
+which is known to improve segmentation algorithm outputs.
 
 Quantitative MRI (qMRI) methods mathematically characterize the signal changes observed in a collection of parametrically altered scans under certain biophysical model assumptions. These `grouped scan collections` are then processed to derive a `qMRI map`, representing anatomical features in a physically meaningful parameter range.
 

From 89387df2700dc27f6c7ef75a3b6f1b2ed24745ea Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Fri, 24 Apr 2020 09:53:54 +0200
Subject: [PATCH 15/76] Some small textual changes

---
 .../01-magnetic-resonance-imaging-data.md                | 9 ++++++---
 1 file changed, 6 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 f2a57df363..dd4db973d5 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
@@ -146,9 +146,12 @@ imaging data, the `_<suffix>` entity can be used in one of three ways:
 3. Quantitative MRI (qMRI) map suffixes
 
 This distinction was added to the specification on acceptance of the BEP001 
-proposal in version `1.x.x`. As a result there are some additional suffixes that
-are no longer recommended but remain part of the specification in order to 
-maintain backwards compatability with previous versions of the specification.
+proposal in version `1.x.x`. However, as a result, some  suffixes that were introduced
+into BIDS at an earlier point time are inconsistent with this typology:
+for example because they are linked to a readout-sequence rather than a contrast, or
+because they don't clearly distinguish between a quantitative map or a contrast-weighted image.
+These `legacy`-suffixes are no longer recommended but remain part of the specification in 
+order to maintain backwards compatability with previous versions of the specification.
 These can be found in the [legacy suffixes](#legacy-suffixes) subsection.
 
 Previous versions of the specification used the term `modality_label` instead of `_suffix` to represent this entity. The change in term was introduced in version 1.x.x. to accodomate a broad definition of anatomical imaging applications.

From f33304d78d512b6e27d33a267f3b2ef901aea3ea Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Fri, 24 Apr 2020 10:56:40 +0200
Subject: [PATCH 16/76] Some small textual changes

---
 .../01-magnetic-resonance-imaging-data.md                | 9 +++++----
 1 file changed, 5 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 09e86bac41..60fdf0e66d 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
@@ -140,7 +140,7 @@ modalities include:
 
 **Function:**
 
-Files that belong to a **grouped scan collection** are intended to be used together within a qMRI analysis framework.
+Files that belong to a **grouped scan collection** are part of a single scan protocol that acquires multiple images with  similar acquisition parameters and is intended to a) increase contrast by combining multiple similar images (e.g., a multi-echo GRE), or b) to estimate physical parameters on an absolute scale, within a qMRI analysis framework (e.g., a T1-map using a MP2RAGE-protocol).
 The quantitative maps that are output from these calculations (e.g., `T1map`, `T2map` etc) are described in the [qMRI map suffixes](#qmri-map-suffixes) section below.
 A change to the specification is REQUIRED to expand or to modify the following table.
 
@@ -150,11 +150,12 @@ A change to the specification is REQUIRED to expand or to modify the following t
 | Inversion recovery (for T1 mapping)        | IRT1    | Grouping | Parametrically linked anatomical images for T1 mapping. The IRT1 method involves multiple inversion recovery spin-echo images acquired at different inversion times. _Associated output suffixes_: T1map, R1map                                                                                                                                                                                                                                                                                                                    |
 | Magnetization prepared two gradient echoes | MP2RAGE | Grouping | Parametrically linked anatomical images (primarily) for T1 mapping. 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. _Associated output suffixes_: T1map, R1map, UNIT1                                                                                                                                                                                                                 |
 | Multi-echo spin echo                       | MESE    | Grouping | Parametrically linked anatomical images (primarily) for T2 mapping.The MESE method involves multiple spin echo images acquired at different echo times. _Associated output suffixes_: T2map, R2map, MWFmap                                                                                                                                                                                                                                                                                                                         |
-| Multi-echo gradient echo                   | MEGRE   | Grouping | Parametrically linked multiple anatomical gradient echo images acquired at different echo times. _Associated output suffixes_: T2starmap, R2starmap, when used for T2* mapping.                                                                                                                                                                                                                                                                                                                                                    |
+| Multi-echo gradient echo                   | MEGRE   | Grouping | Parametrically linked multiple anatomical gradient echo images acquired at different echo times. _Associated output suffixes_: T2starmap, R2starmap                                                                                                                                                                                                                                                                                                                                             |
 | Magnetization transfer ratio               | MTR     | Grouping | Parametrically linked anatomical images for calculating a semi-quantitative magnetization transfer ratio map. _Associated output suffixes_: MTRmap                                                                                                                                                                                                                                                                                                                                                                                 |
 | Magnetization transfer saturation          | MTS     | Grouping | Parametrically linked anatomical images for calculating 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. _Associated output suffixes_: T1map, MTsat                                                                                                                                                                                               |
-| Multi-parametric mapping                   | MPM     | Grouping | Parametrically linked anatomical images for multiparametric mapping (a.k.a hMRI). The MPM method involves anatomical images differing in terms of application of a magnetization transfer RF pulse (MTon or MToff), flip angle and (optionally) echo time and magnitue/phase parts. Please visit [here](https://owncloud.gwdg.de/index.php/s/iv2TOQwGy4FGDDZ) for suggested MPM acquisition protocols.,_Associated output suffixes_:R1map, R2starmap, MTsat, PDmap, T1map, T2starmap                                               |
+| Multi-parametric mapping                   | MPM     | Grouping | Parametrically linked anatomical images for multiparametric mapping (a.k.a hMRI). The MPM approaches 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. See [here](https://owncloud.gwdg.de/index.php/s/iv2TOQwGy4FGDDZ) for suggested MPM acquisition protocols.,_Associated output suffixes_:R1map, R2starmap, MTsat, PDmap, T1map, T2starmap                                               |
 | Double-angle B1 mapping                    | B1DAM   | Grouping | Parametrically linked anatomical images for RF transmit field (B1 plus) mapping. Double angle method is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation angles. Common sequence types for this application include spin echo and echo planar imaging. _Associated output suffixes_: B1plusmap                                                                                                                                                      |
+
 For example:
 
 ```Text
@@ -170,7 +171,7 @@ for each `grouping suffix`.
 Note that every image in a **grouped scan collection** has the same `_<suffix>` 
 as they are likely to be used together.
 Although the acquisitions will have many identical acquisition parameters, only one-to-one-mapping is allowed between a `.json`-sidecar file and an image in a 
-grouped scan collection. This means that parameter values that are identical 
+grouped scan collection. This follows directly from the [inheritance principles of BIDS](../02-common-principles.md#the-inheritance-principle): parameter values that are identical 
 across a set of grouped scans will still have to be stored separately in each `.json`-sidecar file.
 
 Note: Individual images within a grouped scan collection may be used for any purpose.

From 78de563d24ea2ccb105a8036ec3497c4354c053e Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Fri, 24 Apr 2020 11:01:00 +0200
Subject: [PATCH 17/76] Some textual changes

---
 .../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 ed2e1b571d..39d13b669b 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 @@ expand or to modify the following table.
 
 | Name                                                   | _suffix   | _suffix type | Description                                                                                                                                                                                                                                                                          |
 |--------------------------------------------------------|-----------|--------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| Longitudinal relaxation time map                       | T1map     | Parametric   | In seconds (s). T1 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `VFA`, `IRT1`, `MP2RAGE`, `MTS`,`MPM`. You can visit [this interactive book for T1 mapping](https://qmrlab.org/t1_book/intro) for further reading.  |
+| Longitudinal relaxation time map                       | T1map     | Parametric   | In seconds (s). T1 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `VFA`, `IRT1`, `MP2RAGE`, `MTS`,`MPM`. 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     | Parametric   | In seconds (s). T2 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`, `MPM`                                                                                                                                       |
 | Observed transverse relaxation time map                | T2starmap | Parametric   | In seconds (s). T2* maps are REQUIRED to use this suffix irrespective of the method they are related to._Can be generated from:_ `MEGRE`, `MPM`                                                                                                                                      |
 | Longitudinal relaxation rate map                       | R1map     | Parametric   | In seconds-1 (1/s). R1 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `VFA`, `IRT1`, `MP2RAGE`, `MTS`, `MPM`                                                                                                           |
@@ -157,7 +157,7 @@ expand or to modify the following table.
 | Proton density map                                     | PDmap     | Parametric   | In arbitrary units (a.u.). PD maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MPM`                                                                                                                                    |
 | Magnetization transfer ratio map                       | MTRmap    | Parametric   | In percentage (%). MTR maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MTR`                                                                                                                                           |
 | Magnetization transfer saturation index map            | MTsat     | Parametric   | In arbitrary units (a.u.). MTsat maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MTS`, `MPM`                                                                                                                          |
-| Homogeneous (flat) T1 image by MP2RAGE                 | UNIT1     | Parametric   | In arbitrary units (a.u.). UNIT1 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MP2RAGE`                                                                                                                             |
+| Homogeneous (flat) T1-weighted image by MP2RAGE                 | UNIT1     | Parametric   | 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. _Can be generated from:_ `MP2RAGE`                                                                                                                             |
 | Longutidunal relaxation in rotating frame (T1 rho) map | T1rho     | Parametric   | In seconds (s). T1-rho maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ N/A                                                                                                                                             |
 | Myelin water fraction map                              | MWFmap    | Parametric   | In percentage (%). MWF maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`                                                                                                                                          |
 | Combined PD/T2 map                                     | PDT2map   | Parametric   | In arbitrary units (a.u.). Combined PD/T2 maps are REQUIRED to use this suffix irrespective of the method they are related to. N/A                                                                                                                                                   |

From 4edb6f5ab64fc85da9e7401f26a2eb6f7d0c1b3d Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Fri, 8 May 2020 11:51:59 -0400
Subject: [PATCH 18/76] Add temporary doc for conversion

---
 src/99-appendices/09-BEP001-conversion-tmp.md | 115 ++++++++++++++++++
 1 file changed, 115 insertions(+)
 create mode 100644 src/99-appendices/09-BEP001-conversion-tmp.md

diff --git a/src/99-appendices/09-BEP001-conversion-tmp.md b/src/99-appendices/09-BEP001-conversion-tmp.md
new file mode 100644
index 0000000000..547ff23ef5
--- /dev/null
+++ b/src/99-appendices/09-BEP001-conversion-tmp.md
@@ -0,0 +1,115 @@
+> :warning: This `temporary` appendix is intended to provide a conversion guideline between
+different versions of BEP001. 
+
+## Changes to `acq` entity
+
+### Previous convention
+
+In the previous version, the `acq` entity was used to define custom `tags` that 
+specify different combinations of multiple entities:
+
+| Grouping suffix | Labels           | Respective metadata fields and values   |
+|-------------|------------------|------------------------------|
+| MTR         | `MTon`, `MToff`      | MTState [`On`, `Off`] |
+| MTS         | `MTon`, `MToff`, `T1w` | MTstate [`On`,`Off`,`Off`], FlipAngle [`lower`,`lower`,`higher`] |
+| MPM         | `MTon`, `MToff`, `T1w` | MTstate [`On`,`Off`,`Off`], FlipAngle [`lower`,`lower`,`higher`] |
+
+The table above uses `acq` entity to this end for `MTS` and `MTR` by combining 
+two entities (`fa` and non-existing `mt`). 
+
+### New convention
+
+As the previous convention imposed a specific role to a free-from entity, the 
+solution was not ideal and did not receive positive feedback.
+
+To free `acq` tag, we introduced a new entity `mt`, for the suffixes described in BEP001 so far. This limitation applied to `MTR`, `MTS` and `MPM` suffixes. 
+
+These entities will appear in the filenames in the following (alphabetical) order: 
+
+`echo` --> `fa` --> `inv` --> `mt` 
+
+#### Changes for MTR
+
+```diff
+--- MTState on
+- sub-01_acq-MTon_MTR.nii.gz
++ sub-01_mt-on_MTR.nii.gz
+
+
+--- MTState off
+- sub-01_acq-MToff_MTR.nii.gz
++ sub-01_mt-off_MTR.nii.gz
+```
+
+#### Changes for MTS
+
+```diff
+
+--- MTState on | FlipAngle lower
+------ a.k.a MTw
+- sub-01_acq-MTon_MTS.nii.gz
++ sub-01_fa-1_mt-on_MTS.nii.gz
+
+
+--- MTState off | FlipAngle lower
+------ a.k.a PDw
+- sub-01_acq-MToff_MTS.nii.gz
++ sub-01_fa-1_mt-off_MTS.nii.gz
+
+
+--- MTState off | FlipAngle higher
+------ a.k.a T1w
+- sub-01_acq-T1w_MTS.nii.gz
++ sub-01_fa-2_mt-off_MTS.nii.gz
+```
+
+> :warning: **fa-2 > fa-1**
+
+#### Changes for MPM
+```diff
+
+--- MTState on | FlipAngle lower | Echo 1
+------ a.k.a MTw
+- sub-01_echo-1_acq-MTon_MPM.nii.gz
++ sub-01_echo-1_fa-1_mt-on_MPM.nii.gz
+
+
+--- MTState off | FlipAngle lower | Echo 1
+------ a.k.a PDw
+- sub-01_echo-1_acq-MToff_MPM.nii.gz
++ sub-01_echo-1_fa-1_mt-off_MPM.nii.gz
+
+
+--- MTState off | FlipAngle higher | Echo 1
+------ a.k.a T1w
+- sub-01_echo-1_acq-T1w_MPM.nii.gz
++ sub-01_echo-1_fa-2_mt-off_MPM.nii.gz
+```
+
+> :warning: **fa-2 > fa-1**
+
+### Other considerations
+
+#### `RepetitionTime` --> `RepetitionTimeExcitation`
+
+Please use `RepetitionTimeExcitation` for `TR` in anatomical imaging data json files. 
+
+For anatomical acquisitions with multiple readout blocks within a `TR` (e.g. `MP2RAGE`), `RepetitionTimeExcitation` is used along with `RepetitionTimePreparation`.  
+
+#### Ordering of the `metadata` values with respect to the `index` 
+
+##### Ascending order indexing 
+|entity| respective `EchoTime` value in JSON|
+|-------------|------------------|
+|echo-1|          0.005        | 
+|echo-2|          0.010        | 
+|echo-3|          0.015        | 
+etc. 
+
+|entity| respective `FlipAngle` value in JSON|
+|-------------|------------------|
+|fa-1|          5        |
+|fa-2|          25       |
+etc.
+
+> :warning: Indexes MUST correspond to the same value throughout the dataset. For example, `fa-2` MUST NOT point to `FlipAngle = 5` for `echo-1` and to something else (e.g. `FlipAngle = 25`) for `echo-2`.
\ No newline at end of file

From 86fa328ffcd1cc3d8a29e0969e0173ab332cdc7b Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Fri, 8 May 2020 12:02:49 -0400
Subject: [PATCH 19/76] mkdoc

---
 mkdocs.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/mkdocs.yml b/mkdocs.yml
index 24acea42cf..c71448f953 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -42,6 +42,7 @@ nav:
         - MEG file formats: 99-appendices/06-meg-file-formats.md
         - MEG systems: 99-appendices/07-meg-systems.md
         - Coordinate systems: 99-appendices/08-coordinate-systems.md
+        - BEP001: 99-appendices/09-BEP001-conversion-tmp.md
       - Changelog: CHANGES.md
     - The BIDS Starter Kit:
       - GitHub repository: https://github.com/bids-standard/bids-starter-kit

From fd107f42e93706c9dd848410e77c112fd313ac21 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Fri, 8 May 2020 12:12:56 -0400
Subject: [PATCH 20/76] Update 09-BEP001-conversion-tmp.md

---
 src/99-appendices/09-BEP001-conversion-tmp.md | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/src/99-appendices/09-BEP001-conversion-tmp.md b/src/99-appendices/09-BEP001-conversion-tmp.md
index 547ff23ef5..875c3d2404 100644
--- a/src/99-appendices/09-BEP001-conversion-tmp.md
+++ b/src/99-appendices/09-BEP001-conversion-tmp.md
@@ -90,13 +90,13 @@ These entities will appear in the filenames in the following (alphabetical) orde
 
 ### Other considerations
 
-#### `RepetitionTime` --> `RepetitionTimeExcitation`
+#### 1) `RepetitionTime` --> `RepetitionTimeExcitation`
 
 Please use `RepetitionTimeExcitation` for `TR` in anatomical imaging data json files. 
 
 For anatomical acquisitions with multiple readout blocks within a `TR` (e.g. `MP2RAGE`), `RepetitionTimeExcitation` is used along with `RepetitionTimePreparation`.  
 
-#### Ordering of the `metadata` values with respect to the `index` 
+#### 2) Ordering of the `metadata` values with respect to the `index` 
 
 ##### Ascending order indexing 
 |entity| respective `EchoTime` value in JSON|
@@ -112,4 +112,8 @@ etc.
 |fa-2|          25       |
 etc.
 
-> :warning: Indexes MUST correspond to the same value throughout the dataset. For example, `fa-2` MUST NOT point to `FlipAngle = 5` for `echo-1` and to something else (e.g. `FlipAngle = 25`) for `echo-2`.
\ No newline at end of file
+> :warning: Indexes MUST correspond to the same value throughout the dataset. For example, `fa-2` MUST NOT point to `FlipAngle = 5` for `echo-1` and to something else (e.g. `FlipAngle = 25`) for `echo-2`.
+
+#### 3) `index` numeric format 
+
+Use format `%03d` (`001`,`002`,etc) instead of `%d` (`1`,`2`,etc.) for better listing. 

From 34b30041d930cf6fb7a538271fd62fb05b03001e Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 09:24:34 -0400
Subject: [PATCH 21/76] [FIX] Excluded by mistake while resolving conflicts

---
 .../01-magnetic-resonance-imaging-data.md     | 24 +++++++++++++++++++
 1 file changed, 24 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 bf7aefd8c0..273d6b9516 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
@@ -160,6 +160,30 @@ applications, the suffixes will correspond to common anatomical contrasts `T1w`,
 `T2w`, `T2starw` etc. For groups of scans acquired for contrast improvement or 
 qMRI processing, the `_<suffix>` indicates the collection that the scans belong to.
 
+#### The `_<suffix>` entity
+
+To ensure an comprehensible, human readable directory that contains anatomical 
+imaging data, the `_<suffix>` entity can be used in one of three ways:
+
+1. Conventional MRI suffixes
+2. Grouping suffixes
+3. Quantitative MRI (qMRI) map suffixes
+
+This distinction was added to the specification on acceptance of the BEP001 
+proposal in version `1.x.x`. However, as a result, some  suffixes that were introduced
+into BIDS at an earlier point time are inconsistent with this typology: for example 
+because they are linked to a readout-sequence rather than a contrast, or because 
+they don't clearly distinguish between a quantitative map or a contrast-weighted 
+image. These `legacy`-suffixes are no longer recommended but remain part of the 
+specification in order to maintain backwards compatability with previous versions 
+of the specification.
+
+These can be found in the [legacy suffixes](#legacy-suffixes) subsection.
+
+Previous versions of the specification used the term `modality_label` instead of 
+`_suffix` to represent this entity. The change in term was introduced in version 
+`1.x.x.` to accodomate a broad definition of anatomical imaging applications.
+
 #### The `run` entity
 
 If several scans of the same modality are acquired they MUST be indexed with a

From e5420db01192c4b3e1b204729f599a9010802d48 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 09:28:41 -0400
Subject: [PATCH 22/76] [FIX] Merge conflict mess up

* Substitute commit to #6, including changes by @gilles86.
---
 .../01-magnetic-resonance-imaging-data.md     | 51 +++++++++++++++++++
 1 file changed, 51 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 273d6b9516..c3eed94d6e 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
@@ -184,6 +184,57 @@ Previous versions of the specification used the term `modality_label` instead of
 `_suffix` to represent this entity. The change in term was introduced in version 
 `1.x.x.` to accodomate a broad definition of anatomical imaging applications.
 
+##### Conventional MRI suffixes
+
+**Function:**
+
+Denotes the type of the predominant contrast conveyed by an individual file of
+a conventional anatomical image.
+One of the `_<suffix>` entries listed in the table below
+is REQUIRED (with additional entities where applicable) to provide a self-explanatory 
+file name.
+
+A change to the specification is REQUIRED to expand or to modify the following table.
+
+| Name                                       | _suffix | _suffix type | Description                                                                                                                                                                                                                     |
+|--------------------------------------------|---------|--------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| T1 weighted images                         | T1w     | Conventional | Denotes images with predominant T1 contribution.                                                                                                                                                                                |
+| T2 weighted images                         | T2w     | Conventional | Denotes images with predominant T2 contribution.                                                                                                                                                                                |
+| Proton density weighted images             | PDw     | Conventional | Denotes images with predominant proton density (PD) contribution.                                                                                                                                                               |
+| T2 star weighted images                    | T2starw | Conventional | Denotes images with predominant T2* contribution, typically images acquired using a GRE sequence with low flip angle, long echo time and long repetition time. Please note that this suffix is not a surrogate for `T2starmap`. |
+| Fluid Attenuated Inversion Recovery Images | FLAIR   | Conventional | Denotes 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 | Conventional | T1-weighted anatomical image matched to functional acquisition                                                           |
+| Inplane T2                                 | inplaneT2 | Conventional | T2-weighted anatomical image matched to functional acquisition                                                           | 
+
+Example use for conventional **T1 weighted images**:
+
+```Text
+sub-01_run-1_T1w.nii.gz
+sub-01_run-1_T1w.json
+sub-01_run-2_T1w.nii.gz
+sub-01_run-2_T1w.json
+```
+
+The `run` entity in the example above denotes the index of the acquisition
+repeated with the identical scan parameters (e.g., to achieve a higher SNR by averaging the scans together).
+Note that changing parameters between multiple acquisitions of the same sequence
+creates a different use case: **grouped scan collections**. For more information see
+the [grouping suffixes](#grouping-suffixes) subsection.
+
+**Important:**
+
+If an anatomical image is defaced for anonymization, one MAY provide
+the binary mask that was used to remove facial features. In the specific case of
+naming this binary mask, the `_<suffix>` entity is replaced by `_<defacemask>` entry.
+Therefore, to contain the original `_<suffix>` entry, the OPTIONAL `mod-<suffix>`
+entity is used. For example, deface mask image belonging to a **T1 weighted image**
+is named as follows:
+
+```
+sub-01_mod-T1w_defacemask.nii.gz
+sub-01_mod-T1w_defacemask.json
+```
+
 #### The `run` entity
 
 If several scans of the same modality are acquired they MUST be indexed with a

From c34f5a91ac6dce5d82964b7cb8ddd56a166cbf8d Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 09:40:38 -0400
Subject: [PATCH 23/76] suggestion by @gilles86

---
 .../01-magnetic-resonance-imaging-data.md                     | 4 ----
 1 file changed, 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 b9291c0e85..518114bbb8 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
@@ -272,10 +272,6 @@ Although the acquisitions will have many identical acquisition parameters, only
 grouped scan collection. This follows directly from the [inheritance principles of BIDS](../02-common-principles.md#the-inheritance-principle): parameter values that are identical 
 across a set of grouped scans will still have to be stored separately in each `.json`-sidecar file.
 
-Note: Individual images within a grouped scan collection may be used for any purpose.
-For example, the acquisition that is most similar to a `T1w` image may be used in analysis pipelines needing a conventional T1-weighted image.
-
-
 #### The `run` entity
 
 If several scans of the same modality are acquired they MUST be indexed with a

From 4527b17492397c6b76e9438c9f7dd9b856280301 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 09:56:02 -0400
Subject: [PATCH 24/76] Reference implementations

---
 .../01-magnetic-resonance-imaging-data.md            | 12 ++++++------
 1 file changed, 6 insertions(+), 6 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 518114bbb8..0fc66c5cb5 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
@@ -244,15 +244,15 @@ A change to the specification is REQUIRED to expand or to modify the following t
 
 | Name                                       | Suffix  | Type     | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
 |--------------------------------------------|---------|----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| Variable flip angle                        | VFA     | Grouping | Parametrically linked anatomical images (primarily) for relaxometry mapping. 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. Please visit the [qMRI appendix](#prioritylevels) for details. _Associated output suffixes_: T1map, T2map, R1map, R2map |
-| Inversion recovery (for T1 mapping)        | IRT1    | Grouping | Parametrically linked anatomical images for T1 mapping. The IRT1 method involves multiple inversion recovery spin-echo images acquired at different inversion times. _Associated output suffixes_: T1map, R1map                                                                                                                                                                                                                                                                                                                    |
-| Magnetization prepared two gradient echoes | MP2RAGE | Grouping | Parametrically linked anatomical images (primarily) for T1 mapping. 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. _Associated output suffixes_: T1map, R1map, UNIT1                                                                                                                                                                                                                 |
+| Variable flip angle                        | VFA     | Grouping | Parametrically linked anatomical images (primarily) for relaxometry mapping. 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)). Please visit the [qMRI appendix](#prioritylevels) for details. _Associated output suffixes_: T1map, T2map, R1map, R2map |
+| Inversion recovery (for T1 mapping)        | IRT1    | Grouping | Parametrically linked anatomical images for 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)). _Associated output suffixes_: T1map, R1map                                                                                                                                                                                                                                                                                                                    |
+| Magnetization prepared two gradient echoes | MP2RAGE | Grouping | Parametrically linked anatomical images (primarily) for T1 mapping. 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)). _Associated output suffixes_: T1map, R1map, UNIT1                                                                                                                                                                                                                 |
 | Multi-echo spin echo                       | MESE    | Grouping | Parametrically linked anatomical images (primarily) for T2 mapping.The MESE method involves multiple spin echo images acquired at different echo times. _Associated output suffixes_: T2map, R2map, MWFmap                                                                                                                                                                                                                                                                                                                         |
 | Multi-echo gradient echo                   | MEGRE   | Grouping | Parametrically linked multiple anatomical gradient echo images acquired at different echo times. _Associated output suffixes_: T2starmap, R2starmap                                                                                                                                                                                                                                                                                                                                             |
 | Magnetization transfer ratio               | MTR     | Grouping | Parametrically linked anatomical images for calculating a semi-quantitative magnetization transfer ratio map. _Associated output suffixes_: MTRmap                                                                                                                                                                                                                                                                                                                                                                                 |
-| Magnetization transfer saturation          | MTS     | Grouping | Parametrically linked anatomical images for calculating 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. _Associated output suffixes_: T1map, MTsat                                                                                                                                                                                               |
-| Multi-parametric mapping                   | MPM     | Grouping | Parametrically linked anatomical images for multiparametric mapping (a.k.a hMRI). The MPM approaches 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. See [here](https://owncloud.gwdg.de/index.php/s/iv2TOQwGy4FGDDZ) for suggested MPM acquisition protocols.,_Associated output suffixes_:R1map, R2starmap, MTsat, PDmap, T1map, T2starmap                                               |
-| Double-angle B1 mapping                    | B1DAM   | Grouping | Parametrically linked anatomical images for RF transmit field (B1 plus) mapping. Double angle method is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation angles. Common sequence types for this application include spin echo and echo planar imaging. _Associated output suffixes_: B1plusmap                                                                                                                                                      |
+| Magnetization transfer saturation          | MTS     | Grouping | Parametrically linked anatomical images for calculating 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)). _Associated output suffixes_: T1map, MTsat                                                                                                                                                                                               |
+| Multi-parametric mapping                   | MPM     | Grouping | Parametrically linked anatomical images for multiparametric mapping (a.k.a hMRI). The MPM approaches 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.,_Associated output suffixes_:R1map, R2starmap, MTsat, PDmap, T1map, T2starmap                                               |
+| Double-angle B1 mapping                    | B1DAM   | Grouping | Parametrically linked anatomical images for RF transmit field (B1 plus) mapping ([Insko and Bolinger 1993](https://www.sciencedirect.com/science/article/abs/pii/S1064185883711332)). Double angle method is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation angles. Common sequence types for this application include spin echo and echo planar imaging. _Associated output suffixes_: B1plusmap                                                                                                                                                      |
 
 For example:
 

From 6daed428e73b440677ccf9caa25e071917ca0342 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 10:08:15 -0400
Subject: [PATCH 25/76] [FIX] Entity title

---
 .../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 1f238caecc..9e6f80600a 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
@@ -160,7 +160,7 @@ applications, the suffixes will correspond to common anatomical contrasts `T1w`,
 `T2w`, `T2starw` etc. For groups of scans acquired for contrast improvement or 
 qMRI processing, the `_<suffix>` indicates the collection that the scans belong to.
 
-#### The `_<suffix>` entity
+#### The `_suffix` entity
 
 To ensure an comprehensible, human readable directory that contains anatomical 
 imaging data, the `_<suffix>` entity can be used in one of three ways:

From 41d79592a26848c6b318e6d4b41bb486fb78019d Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 10:15:11 -0400
Subject: [PATCH 26/76] [ADD] Appendix for quantitative MRI

* Method specific priority levels
* Deriving new qMRI methods
---
 mkdocs.yml                   |   1 +
 src/99-appendices/10-qmri.md | 172 +++++++++++++++++++++++++++++++++++
 2 files changed, 173 insertions(+)
 create mode 100644 src/99-appendices/10-qmri.md

diff --git a/mkdocs.yml b/mkdocs.yml
index c71448f953..4d6003b48d 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -42,6 +42,7 @@ nav:
         - MEG file formats: 99-appendices/06-meg-file-formats.md
         - MEG systems: 99-appendices/07-meg-systems.md
         - Coordinate systems: 99-appendices/08-coordinate-systems.md
+        - qMRI: 99-appendices/10-qmri.md
         - BEP001: 99-appendices/09-BEP001-conversion-tmp.md
       - Changelog: CHANGES.md
     - The BIDS Starter Kit:
diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
new file mode 100644
index 0000000000..973922e5c4
--- /dev/null
+++ b/src/99-appendices/10-qmri.md
@@ -0,0 +1,172 @@
+### qMRI method-specific priority levels for grouping suffix
+
+Although there is not an upper limit to the amount of metadata
+for images collected by a `grouping suffix`, some of the metadata entries become
+REQUIRED when considered within the context of a specific qMRI
+application.
+
+<a name="prioritylevels">Table of method-specific priority levels for qMRI metadata</a>
+
+| Grouping suffix | REQUIRED metadata                                                                                    | OPTIONAL metadata          |
+|-----------------|------------------------------------------------------------------------------------------------------|----------------------------|
+| VFA             | `FlipAngle`, `PulseSequenceType`, `RepetitionTimeExcitation`                                         | `SpoilingRFPhaseIncrement` |
+| IRT1            | `InversionTime`                                                                                      |                           |
+| MP2RAGE         | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreperation`, `NumberShots` | `EchoTime`                 |
+| MESE            | `EchoTime`                                                                                           |                           |
+| MEGRE           | `EchoTime`                                                                                           |                           |
+| MTR             | `MTState`                                                                                            |                           |
+| MTS             | `FlipAngle`, `MTState`, `RepetitionTimeExcitation`                                                   |                           |
+| MPM             | `FlipAngle`, `MTState`, `RepetitionTimeExcitation`                                                   | `EchoTime`                 |
+| B1DAM           | `FlipAngle`                                                                                          |                          |
+
+Explanation of the table:
+
+* The metadata fields listed in the REQUIRED column are needed to perform a
+minimum viable qMRI application for the corresponding `grouping suffix`.
+* Note that some of the metadata fields may be unaltered across different members
+of a given `grouped scan collection`, yet still needed as an input to a qMRI
+model for parameter fitting (e.g. `RepetitionTimeExcitation` of `VFA`). 
+* The metadata fields listed in the OPTIONAL column can be used to derive
+various qMRI applications from an existing `grouping suffix`. The following section expands on the set of rules to derive qMRI applications from an existing `grouping suffix`.
+
+### qMRI applications that can be derived from an existing `grouping suffix`
+
+Certain grouping 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 varying additional scan parameters.
+
+If such inheritance relationship is applicable between an already existing
+`grouping suffix` and a new qMRI application to be included in the specification,
+the inheritor qMRI method MUST be listed in the table below instead of
+introducing a new `grouping suffix`. This approach:
+
+* prevents the list of available suffixes from over-proliferation
+* provides qMRI-focused BIDS applications with a set of meta-data driven rules
+to infer possible fitting options
+* keep an inheritance track of the qMRI methods described within the
+specification.
+
+<a name="varianttable">Table of qMRI applications that can be derived from an existing grouping suffix</a>
+
+| Grouping suffix | If REQUIRED metadata == Value | OPTIONAL metadata [`var`/`fix`]<sup>[*](#footnotederive)</sup>      | Derived application |
+|-----------------|-------------------------------|----------------------------------|---------------------|
+| VFA             | `PulseSequenceType` == `SPGR` |                                  | DESPOT1             |
+| VFA             | `PulseSequenceType` == `SSFP` | `SpoilingRFPhaseIncrement` [`fix`] | DESPOT2             |
+| VFA             | `PulseSequenceType` == `SSFP` | `SpoilingRFPhaseIncrement` [`var`] | DESPOT2-FM          |
+| MP2RAGE         |                               | `EchoTime` [`var`]                 | MP2RAGE-ME          |
+| MPM             |                               | `EchoTime` [`var`]                 | MPM-ME              |
+
+<a name="footnotederive">*</a> `var` denotes that the listed OPTIONAL metadata value changes across
+ constituent images of the respective `grouping suffix`, fixed otherwise (`fix`). 
+ If the OPTIONAL metadata type is `var`, respective naming entities can be found in the 
+ OPTIONAL entities column of [`grouping suffix` table](#grouping-suffix). 
+*** 
+
+A derived qMRI application becomes avaiable if all the OPTIONAL metadata fields
+listed for a `grouping suffix` is provided in 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 `grouping suffix`. 
+
+For example, if the REQUIRED 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. Finally, if the `DESPOT2` data has more than one
+`SpoilingRFPhaseIncrement` field as a metadata field, then the dataset is valid
+for `DESPOT2-FM`. In this case, `rfphase` entity can be used to distinguish inputs. 
+
+Please note that OPTIONAL metadata fields listed in the [qMRI applications that can be derived from an existing suffix table](#varianttable) MUST be also included in the [method sprecific priority levels for qMRI metadata table](#prioritylevels)  for the sake of completeness.
+
+Please also note that the rules concerning the presence/value of certain metadata
+fields within the context of `grouping suffix` is not a part of the BIDS
+validation process. Such rules rather constitute a centralized guideline for
+creating interoperable qMRI datasets.
+
+For a dataset with a `grouping suffix`, the BIDS validation is successful if:
+
+* provided NIfTI and JSON file names respect the anatomy imaging dataset template
+* provided suffixes are present in the list of available suffixes
+* sidecar JSON files follow the hierarchy defined for `grouping suffix`.
+
+### Metadata of qMRI maps
+
+Metadata fields listed in the sidecar JSON of a qMRI map depend on the method by
+which it is obtained:
+* If a qMRI map is generated at the scanner site through non-transparent vendor
+implementation, JSON content is confined to the available metadata.
+* If a qMRI map is generated using an open-source software, its sidecar JSON
+file MUST inherit content from the JSON files of the constituent images of a
+`grouped scan collection` by adhering to the following rules:
+     * All the acquisition parameters that are unchanged across constituents of
+     a `grouped scan collection` are added to the JSON file of the resultant
+     qMRI map.
+     * Relevant acquisition parameters that vary across constituents of a
+     `grouped scan collection` are added to the JSON file of the resultant
+     qMRI map **in array form**. To find out which varying scan parameters are
+     relevant to a given `grouped scan collection`, please see the
+    [method-specific priority levels for qMRI metadata](#prioritylevels) above.
+     * The JSON file accompanying a qMRI map which is obtained by
+     using an open-source software MUST include all the metadata fields listed
+     in the following table for the sake of provenance.
+
+| Field name                  | Definition                                                     |
+| :-------------------------- | :------------------------------------------------------------- |
+| BasedOn | List of files grouped by an `grouping suffix` to generate the map. The 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.)|
+| EstimationSoftwareName | The name of the open-source tool used for fitting (e.g. qMRLab, QUIT, hMRI-Toolbox etc.)|
+| EstimationSoftwareVer | Version of the open-source tool used for fitting (e.g. v2.3.0 etc.)|
+| EstimationSoftwareLang | Language in which the software is natively developed (e.g. MATLAB R2018b, C++17, Python 3.6 etc.)|
+| EstimationSoftwareEnv | Operation system on which the application was run (e.g. OSX 10.14.3, Ubuntu 18.04, Win10 etc.)|
+
+Example:
+
+```Text
+sub-01_T1map.nii.gz
+sub-01_T1map.json
+```
+
+```Text
+sub-01_T1map.json
+{
+
+<<Parameter injected by the software for provenance recording>>
+
+"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_B1plusmap.nii.gz"],
+
+<<Parameters that are constant across members of VFA grouping suffix>>
+
+“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 members of VFA grouping suffix>>
+
+"FlipAngle": ["5","10","15","20"],
+
+<<Additional parameters injected by the software for provenance recording>>
+
+"EstimationPaper":"Deoni et. al.MRM, 2015",
+"EstimationAlgorithm":"Linear",
+“EstimationSoftwareName”: “qMRLab”,
+“EstimationSoftwareLanguage”: “Octave”,
+“EstimationSoftwareVersion”: “2.3.0”,
+“EstimationSoftwareEnv”: “Ubuntu 16.04”
+}
+```\
\ No newline at end of file

From e5068b3ebd09f9acf0ac20323fb08da83bd41b2a Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 10:18:46 -0400
Subject: [PATCH 27/76] [ENH] Entity table for qMRI

---
 src/99-appendices/04-entity-table.md | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 11e485f9dd..ab0c68550f 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -30,3 +30,19 @@ A general introduction to entities is given in the section on
 | photo<br>(meg/eeg/ieeg)                                                                        | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          |               |                        |                |                     |                       |                 |        
 | electrodes<br>(eeg/ieeg)                                                                       | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          |               |                        |                |                     |                       | OPTIONAL        |
 | events<br>(meg/eeg/ieeg)                                                                       | REQUIRED      | OPTIONAL      | REQUIRED       |               |                          |                |                          | OPTIONAL      |                        |                |                     |                       |                 |        
+
+> :warning: The following entity table is suggested by BEP001 [WIP]. If convenient, 
+to be merged to the table above.
+
+| Entity                                                                                                     | Subject       | Session       | Task           | Acquisition   | Contrast Enhancing Agent | Reconstruction | Phase-Encoding Direction | Run           | Corresponding Modality | Echo           | Flip Angle   | Inversion Time | Magnetization Transfer | Part               | Recording           | Processed      | Space           |
+|------------------------------------------------------------------------------------------------------------|---------------|---------------|----------------|---------------|--------------------------|----------------|--------------------------|---------------|------------------------|----------------|--------------|----------------|------------------------|--------------------|---------------------|----------------|-----------------|
+| Format                                                                                                     | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`             | `rec-<label>`  | `dir-<label>`            | `run-<index>` | `mod-<suffix>`         | `echo-<index>` | `fa-<index>` | `inv-<index>`  | `mt-<on/off>`          | `part-<mag/phase>` | `recording-<label>` | `proc-<label>` | `space-<label>` |
+| anat (T1w T2w  PDw T2starw  FLASH inplaneT1  inplaneT2)                                                    | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        |                |              |                |                        | OPTIONAL           |                     |                |                 |
+| anat (defacemask)                                                                                          | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      | OPTIONAL               |                |              |                |                        |                    |                     |                |                 |
+| anat (T1map T2map T2starmap R1map R2map R2starmap PDmap MTRmap MTsat UNIT1 T1rho MWFmap PDT2map B1plusmap) | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        |                |              |                |                        |                    |                     |                |                 |
+| anat (MESE MGRE)                                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        | REQUIRED       |              |                |                        | OPTIONAL           |                     |                |                 |
+| anat (VFA B1DAM)                                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        |                | REQUIRED     |                |                        | OPTIONAL           |                     |                |                 |
+| anat (MP2RAGE)                                                                                             | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        | OPTIONAL       | REQUIRED     | REQUIRED       |                        | OPTIONAL           |                     |                |                 |
+| anat (MPM MTS)                                                                                             | REQURED       | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        | OPTIONAL       | REQUIRED     |                | REQUIRED               | OPTIONAL           |                     |                |                 |
+| anat (MTR)                                                                                                 | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        |                |              |                | REQUIRED               | OPTIONAL           |                     |                |                 |
+| anat (IRT1)                                                                                                | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        |                |              | REQUIRED       |                        | OPTIONAL           |                     |                |                 |
\ No newline at end of file

From 5b850500097432917face714663ea08e74e85cb2 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 10:36:09 -0400
Subject: [PATCH 28/76] [FIX] Typo

---
 src/99-appendices/10-qmri.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index 973922e5c4..a72e18cdde 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -130,7 +130,7 @@ sub-01_T1map.nii.gz
 sub-01_T1map.json
 ```
 
-```Text
+```
 sub-01_T1map.json
 {
 
@@ -169,4 +169,4 @@ sub-01_T1map.json
 “EstimationSoftwareVersion”: “2.3.0”,
 “EstimationSoftwareEnv”: “Ubuntu 16.04”
 }
-```\
\ No newline at end of file
+```

From 6a62384b7743098a75d9e496062eddffc10f93ed Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 10:46:24 -0400
Subject: [PATCH 29/76] PR 24 from old repository

*  This pull-request was opened and merged by @KirstieJane
* https://github.com/bids-standard/bep001/pull/24/files#
---
 .../01-magnetic-resonance-imaging-data.md                     | 4 +++-
 1 file changed, 3 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 9e6f80600a..c74fd3f330 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
@@ -365,6 +365,8 @@ fields specific to anatomical scans:
 | Field name              | Definition                                                                                                                                         |
 | -----------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------- |
 | ContrastBolusIngredient | OPTIONAL. Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048. |
+| RepetitionTimeExcitation | OPTIONAL. The time in seconds between successive excitation pulses that excite the same tissue. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be superseded by `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://infoscience.epfl.ch/record/172927/files/mp2rage.pdf). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in section 4.1.x. |
+| RepetitionTimePreparation | OPTIONAL. The period of time in seconds that it takes a preparation pulse block to re-appear at the beginning of the succeeding (essentially identical) pulse sequence. |
 
 ##### Legacy suffixes (to be deprecated)
 
@@ -463,7 +465,7 @@ JSON file.
 
 | Field name     | Definition                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
 |-----------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| RepetitionTime | REQUIRED. The time in seconds between the beginning of an acquisition of one volume and the beginning of acquisition of the volume following it (TR). Please note that this definition includes time between scans (when no data has been acquired) in case of sparse acquisition schemes. This value needs to be consistent with the `pixdim[4]` field (after accounting for units stored in `xyzt_units` field) in the NIfTI header. This field is mutually exclusive with `VolumeTiming` and is derived from DICOM Tag 0018, 0080 and converted to seconds. |
+| RepetitionTime | REQUIRED. The time in seconds between the beginning of an acquisition of one volume and the beginning of acquisition of the volume following it (TR). When used in the context of functional acquisitions this parameter best corresponds to [DICOM Tag 0020,0110](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0020,0110)): the "time delta between images in a dynamic of functional set of images" but may be found in [DICOM Tag 0018, 0080](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)): "the period of time in msec between the beginning of a pulse sequence and the beginning of the succeeding (essentially identical) pulse sequence". This definition includes time between scans (when no data has been acquired) in case of sparse acquisition schemes. This value MUST be consistent with the '`pixdim[4]`' field (after accounting for units stored in '`xyzt_units`' field) in the NIfTI header. This field is mutually exclusive with `VolumeTiming`. |
 | VolumeTiming   | REQUIRED. The time at which each volume was acquired during the acquisition. It is described using a list of times (in JSON format) referring to the onset of each volume in the BOLD series. The list must have the same length as the BOLD series, and the values must be non-negative and monotonically increasing. This field is mutually exclusive with `RepetitionTime` and `DelayTime`. If defined, this requires acquisition time (TA) be defined via either `SliceTiming` or `AcquisitionDuration` be defined.                                        |
 | TaskName       | REQUIRED. Name of the task. No two tasks should have the same name. Task label (`task-`) included in the file name is derived from this field by removing all non alphanumeric (`[a-zA-Z0-9]`) characters. For example task name `faces n-back` will corresponds to task label `facesnback`. A RECOMMENDED convention is to name resting state task using labels beginning with `rest`.                                                                                                                                                                        |
 

From f2cb0ea2a07f702a19afb93ef5fbb7b6812a9c2d Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 11:03:29 -0400
Subject: [PATCH 30/76] [ADD] The part entity

---
 .../01-magnetic-resonance-imaging-data.md              | 10 ++++++++++
 1 file changed, 10 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 c74fd3f330..c4c40cea31 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
@@ -315,6 +315,16 @@ with the unit description provided for its respective `_suffix` entry.
 For example, a T1 map in milliseconds unit (ms) is not valid, given that the
 description of the `T1map` suffix requires the parameter to be in seconds (s).
 
+#### The `part` entity
+
+Some applications depends on `magnitude` and `phase` reconstructed images for the 
+calculation of a parameter map. In such case two files could have the following 
+names: `sub-01_part-mag_T1w.nii.gz` and `sub-01_part-phase_T1w.nii.gz`. 
+
+Phase images SHOULD be in radians and have a range of (0, 2 pi] (including 0, 
+excluding 2 pi). The `part-<mag/phase>` key/value pair is associated with the 
+DICOM tag [0008,9208](https://dicom.innolitics.com/ciods/enhanced-mr-image/enhanced-mr-image/00089208).
+
 #### The `run` entity
 
 If several scans of the same modality are acquired they MUST be indexed with a

From 3d3cc62cccaf701868b15222e936cbf62ec82e72 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 11:10:08 -0400
Subject: [PATCH 31/76] [ADD] Additional metadata for anatomical images

* https://github.com/bids-standard/bep001/pull/30/files#diff-d668661006216379ab2a5c5ff7061b8aR40-R50
---
 .../01-magnetic-resonance-imaging-data.md             | 11 +++++++++++
 1 file changed, 11 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 c74fd3f330..2a7825ccd2 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
@@ -37,6 +37,17 @@ by Ben Inglis:
 | SequenceName                | RECOMMENDED. Manufacturer’s designation of the sequence name. Corresponds to DICOM Tag 0018, 0024 `Sequence Name`.                                                                                                                                                             |
 | PulseSequenceDetails        | RECOMMENDED. Information beyond pulse sequence type that identifies the specific pulse sequence used (i.e. "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 stating if the image saved has been corrected for gradient nonlinearities by the scanner sequence.                                                                                                                                                        |
+| MTState           | RECOMMENDED. Boolean value (`true` or `false`), specifying whether the magnetization transfer pulse is applied. This parameter is REQUIRED by all the anatomical images grouped by `MTR`, `MTS` and `MPM` suffixes. This field originally corresponds to DICOM tag 0018, 9020 `Magnetization Transfer`. |
+| MTOffsetFrequency | RECOMMENDED. The frequency offset of the magnetization transfer pulse with respect to the central H1 Larmor frequency in Hertz (Hz).                                                                                                                                                                    |
+| MTPulseBandwidth  | RECOMMENDED. The excitation bandwidth of the magnetization transfer pulse in Hertz (Hz).                                                                                                                                                                                                                |
+| MTNumberOfPulses  | RECOMMENDED. Number of magnetization transfer RF pulses applied before the readout.                                                                                                                                                                                                                     |
+| MTPulseShape      | RECOMMENDED. 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. Duration of the magnetization transfer RF pulse in seconds.                                                                                                                                                                                                                                |
+| SpoilingState            | RECOMMENDED. Boolean value (`true` or `false`), specifying whether the pulse sequence uses any type of spoiling stratey to suppress transverse magnetization remaining after the readout. |
+| SpoilingType             | RECOMMENDED. Specifies which spoiling method(s) are used by a spoiled sequence. Accepted values: `RF`, `GRADIENT` or `COMBINED`.                                                          |
+| SpoilingRFPhaseIncrement | RECOMMENDED. 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. Zeroth moment of the spoiler gradient lobe in militesla times second per meter (mT.s/m).                                                                                     |
+| SpoilingGradientDuration | RECOMMENDED. 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
 

From 39589490f12a323996a3344936eced2cae77e205 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 12:00:54 -0400
Subject: [PATCH 32/76] [ADD] Description about symlinks for qMRI maps

---
 src/99-appendices/10-qmri.md | 76 +++++++++++++++++++++++++++++++-----
 1 file changed, 67 insertions(+), 9 deletions(-)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index a72e18cdde..71ef3d4312 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -92,15 +92,73 @@ For a dataset with a `grouping suffix`, the BIDS validation is successful if:
 * provided suffixes are present in the list of available suffixes
 * sidecar JSON files follow the hierarchy defined for `grouping suffix`.
 
-### Metadata of qMRI maps
-
-Metadata fields listed in the sidecar JSON of a qMRI map depend on the method by
-which it is obtained:
-* If a qMRI map is generated at the scanner site through non-transparent vendor
-implementation, JSON content is confined to the available metadata.
-* If a qMRI map is generated using an open-source software, its sidecar JSON
-file MUST inherit content from the JSON files of the constituent images of a
-`grouped scan collection` by adhering to the following rules:
+### Management of the qMRI maps
+
+All qMRI maps are generated following a set of calculations. Unlike conventional 
+MR images, they are not products of an MRI image reconstruction (from k-space data 
+to structural images). There are two possible options in the way a qMRI map is obtained: 
+
+1. The qMRI map is calculated at the scanner site through a non-transparent vendor pipeline.
+2. The qMRI map is generated off-site using an open-source software. 
+
+#### Where to place qMRI maps? 
+
+**If the qMRI map is calculated at the scanner site through a non-transparent vendor pipeline:** 
+
+Although qMRI maps are derivatives, we cannot relate them to their parent images (which may
+not even be accessible) through a set of calculations in this case. Therefore, such maps obtained
+at the scanner site via non-transparent pipelines are placed at the `/sub-#/anat` directory.
+
+**If the qMRI map is generated using an open-source software:**
+
+Quantitative maps SHOULD be stored in the `derivatives` folder, but MAY
+be symbolic linked to the corresponding raw data directory to facilitate the
+easy use of these images as input to processing workflows implemented as
+BIDS-apps. For example:
+
+```diff
+ ds-example/
+ ├── derivatives/
+ |   └── qMRI-software/
+ |       └── sub-01/
+ |           └── anat/
++|               ├── sub-01_T1map.nii.gz
++|               ├── sub-01_T1map.json
++|               ├── sub-01_MTsat.nii.gz
++|               └── sub-01_MTsat.json
+ ├── sub-01/
+ |   ├── anat/
+ |   |   ├── sub-01_fa-1_mt-on_MTS.nii.gz
+ |   |   ├── sub-01_fa-1_mt-on_MTS.json
+ |   |   ├── sub-01_fa-1_mt-off_MTS.nii.gz
+ |   |   ├── sub-01_fa-1_mt-off_MTS.json
+ |   |   ├── sub-01_fa-2_mt-off_MTS.nii.gz
+ |   |   ├── sub-01_fa-2_mt-off_MTS.json
+-|   |   ├── sub-01_T1map.nii.gz
+-|   |   ├── sub-01_T1map.json
+-|   |   ├── sub-01_MTsat.nii.gz
+-|   |   └── sub-01_MTsat.json
+ |   |
+ |   └──func/..
+ |
+ └── sub-#N/..
+```
+
+In the `diff` styled file tree above, the files highlighted by red are
+symbolic linked to the qMRI outputs (highlighted by green), so that an
+application looking for a qMRI map can locate them under the `sub-01/anat` 
+directory along with other anatomical images. 
+
+#### Which metadata fields should a qMRI map contain? 
+
+**If the qMRI map is calculated at the scanner site through a non-transparent vendor pipeline:** 
+
+JSON content is confined to the metadata made available by the vendor pipeline.
+
+**If the qMRI map is generated using an open-source software:**
+
+JSON file of the qMRI map MUST inherit metadata from its parent images (typically a grouped scan 
+collection) by adhering to the following rules:
      * All the acquisition parameters that are unchanged across constituents of
      a `grouped scan collection` are added to the JSON file of the resultant
      qMRI map.

From 913f984c6e244a3e23d25c4d454202e2e58e4634 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 12:03:06 -0400
Subject: [PATCH 33/76] Update 10-qmri.md

---
 src/99-appendices/10-qmri.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index 71ef3d4312..773db05721 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -128,6 +128,8 @@ BIDS-apps. For example:
 +|               └── sub-01_MTsat.json
  ├── sub-01/
  |   ├── anat/
+ |   |   ├── sub-01_T1w.nii.gz
+ |   |   ├── sub-01_T1w.json
  |   |   ├── sub-01_fa-1_mt-on_MTS.nii.gz
  |   |   ├── sub-01_fa-1_mt-on_MTS.json
  |   |   ├── sub-01_fa-1_mt-off_MTS.nii.gz

From ae46b7aee20d506ad269613842eb4aaba98ad2e5 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 12:26:03 -0400
Subject: [PATCH 34/76] Update 10-qmri.md

---
 src/99-appendices/10-qmri.md | 44 ++++++++++++++++++------------------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index 773db05721..4edf984a98 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -122,34 +122,34 @@ BIDS-apps. For example:
  |   └── qMRI-software/
  |       └── sub-01/
  |           └── anat/
-+|               ├── sub-01_T1map.nii.gz
-+|               ├── sub-01_T1map.json
-+|               ├── sub-01_MTsat.nii.gz
-+|               └── sub-01_MTsat.json
- ├── sub-01/
- |   ├── anat/
- |   |   ├── sub-01_T1w.nii.gz
- |   |   ├── sub-01_T1w.json
- |   |   ├── sub-01_fa-1_mt-on_MTS.nii.gz
- |   |   ├── sub-01_fa-1_mt-on_MTS.json
- |   |   ├── sub-01_fa-1_mt-off_MTS.nii.gz
- |   |   ├── sub-01_fa-1_mt-off_MTS.json
- |   |   ├── sub-01_fa-2_mt-off_MTS.nii.gz
- |   |   ├── sub-01_fa-2_mt-off_MTS.json
--|   |   ├── sub-01_T1map.nii.gz
--|   |   ├── sub-01_T1map.json
--|   |   ├── sub-01_MTsat.nii.gz
--|   |   └── sub-01_MTsat.json
+ |               ├── sub-01_T1map.nii.gz ──────────┐ S
+ |               ├── sub-01_T1map.json   ────────┐ | Y
+ |               ├── sub-01_MTsat.nii.gz ──────┐ | | M
+ |               └── sub-01_MTsat.json   ────┐ | | | L 
+ ├── sub-01/                                 | | | | I
+ |   ├── anat/                               | | | | N
+ |   |   ├── sub-01_T1w.nii.gz               | | | | K
+ |   |   ├── sub-01_T1w.json                 | | | | 
+ |   |   ├── sub-01_fa-1_mt-on_MTS.nii.gz    | | | | T
+ |   |   ├── sub-01_fa-1_mt-on_MTS.json      | | | | O 
+ |   |   ├── sub-01_fa-1_mt-off_MTS.nii.gz   | | | | 
+ |   |   ├── sub-01_fa-1_mt-off_MTS.json     | | | | A
+ |   |   ├── sub-01_fa-2_mt-off_MTS.nii.gz   | | | | N
+ |   |   ├── sub-01_fa-2_mt-off_MTS.json     | | | | A
+ |   |   ├── sub-01_T1map.nii.gz ◀───────────├─├─├─┘ T
+ |   |   ├── sub-01_T1map.json   ◀───────────├─├─┘   
+ |   |   ├── sub-01_MTsat.nii.gz ◀───────────├─┘     
+ |   |   └── sub-01_MTsat.json   ◀───────────┘         
  |   |
  |   └──func/..
  |
  └── sub-#N/..
 ```
 
-In the `diff` styled file tree above, the files highlighted by red are
-symbolic linked to the qMRI outputs (highlighted by green), so that an
-application looking for a qMRI map can locate them under the `sub-01/anat` 
-directory along with other anatomical images. 
+In the example above, outputs of the `MTS` that are placed under `derivatives`
+folder are symbolic linked to the respective `anat` folder, so that an
+application looking for a qMRI map can easily locate them in the same directory
+along with other anatomical images. 
 
 #### Which metadata fields should a qMRI map contain? 
 

From ece994b3d5990267dc7af96a755b35c8a7e76cd3 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 12:29:50 -0400
Subject: [PATCH 35/76] Update 10-qmri.md

---
 src/99-appendices/10-qmri.md | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index 4edf984a98..1f50a242c5 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -1,4 +1,4 @@
-### qMRI method-specific priority levels for grouping suffix
+# Method-specific priority levels for grouping suffix
 
 Although there is not an upper limit to the amount of metadata
 for images collected by a `grouping suffix`, some of the metadata entries become
@@ -29,7 +29,7 @@ model for parameter fitting (e.g. `RepetitionTimeExcitation` of `VFA`).
 * The metadata fields listed in the OPTIONAL column can be used to derive
 various qMRI applications from an existing `grouping suffix`. The following section expands on the set of rules to derive qMRI applications from an existing `grouping suffix`.
 
-### qMRI applications that can be derived from an existing `grouping suffix`
+# qMRI applications that can be derived from an existing `grouping suffix`
 
 Certain grouping suffixes may refer to a generic data collection regime such as
 variable flip angle (VFA), rather than a more specific acquisition, e.g.,
@@ -92,7 +92,7 @@ For a dataset with a `grouping suffix`, the BIDS validation is successful if:
 * provided suffixes are present in the list of available suffixes
 * sidecar JSON files follow the hierarchy defined for `grouping suffix`.
 
-### Management of the qMRI maps
+# Management of the qMRI maps
 
 All qMRI maps are generated following a set of calculations. Unlike conventional 
 MR images, they are not products of an MRI image reconstruction (from k-space data 
@@ -101,7 +101,7 @@ to structural images). There are two possible options in the way a qMRI map is o
 1. The qMRI map is calculated at the scanner site through a non-transparent vendor pipeline.
 2. The qMRI map is generated off-site using an open-source software. 
 
-#### Where to place qMRI maps? 
+## Where to place qMRI maps? 
 
 **If the qMRI map is calculated at the scanner site through a non-transparent vendor pipeline:** 
 
@@ -146,12 +146,11 @@ BIDS-apps. For example:
  └── sub-#N/..
 ```
 
-In the example above, outputs of the `MTS` that are placed under `derivatives`
-folder are symbolic linked to the respective `anat` folder, so that an
-application looking for a qMRI map can easily locate them in the same directory
-along with other anatomical images. 
+In the example above, outputs of the `MTS` that are placed under the `derivatives`
+folder are symbolic linked to the respective `anat` folder. This way, an
+application can easily pick up a qMRI map along with other anatomical images.
 
-#### Which metadata fields should a qMRI map contain? 
+## Which metadata fields should a qMRI map contain? 
 
 **If the qMRI map is calculated at the scanner site through a non-transparent vendor pipeline:** 
 

From 50bd7abb686442a7f85681beeb6cede5fdbe68d9 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 12:34:25 -0400
Subject: [PATCH 36/76] Update 10-qmri.md

---
 src/99-appendices/10-qmri.md | 25 +++++++++++++------------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index 1f50a242c5..7494360072 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -160,24 +160,25 @@ JSON content is confined to the metadata made available by the vendor pipeline.
 
 JSON file of the qMRI map MUST inherit metadata from its parent images (typically a grouped scan 
 collection) by adhering to the following rules:
-     * All the acquisition parameters that are unchanged across constituents of
-     a `grouped scan collection` are added to the JSON file of the resultant
-     qMRI map.
-     * Relevant acquisition parameters that vary across constituents of a
-     `grouped scan collection` are added to the JSON file of the resultant
-     qMRI map **in array form**. To find out which varying scan parameters are
-     relevant to a given `grouped scan collection`, please see the
-    [method-specific priority levels for qMRI metadata](#prioritylevels) above.
-     * The JSON file accompanying a qMRI map which is obtained by
-     using an open-source software MUST include all the metadata fields listed
-     in the following table for the sake of provenance.
+* All the acquisition parameters that are unchanged across constituents of
+a `grouped scan collection` are added to the JSON file of the resultant
+qMRI map.
+* Relevant acquisition parameters that vary across constituents of a
+`grouped scan collection` are added to the JSON file of the resultant
+qMRI map **`in array form`**. 
+ > To find out which varying scan parameters are
+ relevant to a given `grouped scan collection`, please see the
+[method-specific priority levels for qMRI metadata](#prioritylevels) above.
+* The JSON file accompanying a qMRI map which is obtained by
+using an open-source software MUST include all the metadata fields listed
+in the following table for the sake of provenance.
 
 | Field name                  | Definition                                                     |
 | :-------------------------- | :------------------------------------------------------------- |
 | BasedOn | List of files grouped by an `grouping suffix` to generate the map. The 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.)|
-| EstimationSoftwareName | The name of the open-source tool used for fitting (e.g. qMRLab, QUIT, hMRI-Toolbox etc.)|
+| EstimationSoftwareName | The name of the open-source tool used for fitting (e.g. [qMRLab](https://qmrlab.org), [QUIT](https://github.com/spinicist/QUIT), [hMRI-Toolbox](https://hmri-group.github.io/hMRI-toolbox/) etc.)|
 | EstimationSoftwareVer | Version of the open-source tool used for fitting (e.g. v2.3.0 etc.)|
 | EstimationSoftwareLang | Language in which the software is natively developed (e.g. MATLAB R2018b, C++17, Python 3.6 etc.)|
 | EstimationSoftwareEnv | Operation system on which the application was run (e.g. OSX 10.14.3, Ubuntu 18.04, Win10 etc.)|

From f863f424230be6cfc1e9c8ab632a609ef0e60458 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 12:37:47 -0400
Subject: [PATCH 37/76] [FIX] Indentation difference

---
 src/99-appendices/10-qmri.md | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index 7494360072..9774f90a6c 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -126,16 +126,16 @@ BIDS-apps. For example:
  |               ├── sub-01_T1map.json   ────────┐ | Y
  |               ├── sub-01_MTsat.nii.gz ──────┐ | | M
  |               └── sub-01_MTsat.json   ────┐ | | | L 
- ├── sub-01/                                 | | | | I
- |   ├── anat/                               | | | | N
- |   |   ├── sub-01_T1w.nii.gz               | | | | K
- |   |   ├── sub-01_T1w.json                 | | | | 
- |   |   ├── sub-01_fa-1_mt-on_MTS.nii.gz    | | | | T
- |   |   ├── sub-01_fa-1_mt-on_MTS.json      | | | | O 
- |   |   ├── sub-01_fa-1_mt-off_MTS.nii.gz   | | | | 
- |   |   ├── sub-01_fa-1_mt-off_MTS.json     | | | | A
- |   |   ├── sub-01_fa-2_mt-off_MTS.nii.gz   | | | | N
- |   |   ├── sub-01_fa-2_mt-off_MTS.json     | | | | A
+ ├── sub-01/                                | | | | I
+ |   ├── anat/                              | | | | N
+ |   |   ├── sub-01_T1w.nii.gz              | | | | K
+ |   |   ├── sub-01_T1w.json                | | | | 
+ |   |   ├── sub-01_fa-1_mt-on_MTS.nii.gz   | | | | T
+ |   |   ├── sub-01_fa-1_mt-on_MTS.json     | | | | O 
+ |   |   ├── sub-01_fa-1_mt-off_MTS.nii.gz  | | | | 
+ |   |   ├── sub-01_fa-1_mt-off_MTS.json    | | | | A
+ |   |   ├── sub-01_fa-2_mt-off_MTS.nii.gz  | | | | N
+ |   |   ├── sub-01_fa-2_mt-off_MTS.json    | | | | A
  |   |   ├── sub-01_T1map.nii.gz ◀───────────├─├─├─┘ T
  |   |   ├── sub-01_T1map.json   ◀───────────├─├─┘   
  |   |   ├── sub-01_MTsat.nii.gz ◀───────────├─┘     

From e45d2fbb44436ce09dc128e4915c2c10e2ee1fd4 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 12:43:00 -0400
Subject: [PATCH 38/76] [FIX] Indentation differences xross md and website

---
 src/99-appendices/10-qmri.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index 9774f90a6c..76eb1ef59f 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -122,10 +122,10 @@ BIDS-apps. For example:
  |   └── qMRI-software/
  |       └── sub-01/
  |           └── anat/
- |               ├── sub-01_T1map.nii.gz ──────────┐ S
- |               ├── sub-01_T1map.json   ────────┐ | Y
- |               ├── sub-01_MTsat.nii.gz ──────┐ | | M
- |               └── sub-01_MTsat.json   ────┐ | | | L 
+ |               ├── sub-01_T1map.nii.gz ─────────┐ S
+ |               ├── sub-01_T1map.json   ───────┐ | Y
+ |               ├── sub-01_MTsat.nii.gz ─────┐ | | M
+ |               └── sub-01_MTsat.json   ───┐ | | | L 
  ├── sub-01/                                | | | | I
  |   ├── anat/                              | | | | N
  |   |   ├── sub-01_T1w.nii.gz              | | | | K

From 7a3a121c8830a5ae877ad776e1d674e1feb7201a Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 16:53:57 -0400
Subject: [PATCH 39/76] [ADD] Echo entity

---
 .../01-magnetic-resonance-imaging-data.md     | 25 +++++++++++++++++--
 1 file changed, 23 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 2a7825ccd2..8a8772bc86 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
@@ -124,8 +124,8 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     anat/
-        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_ce-<label>][_rec-<label>][_run-<index>]_<suffix>.nii[.gz]
-        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<suffix>]_defacemask.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_echo-<index>][_ce-<label>][_rec-<label>][_run-<index>]_<suffix>.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_echo-<index>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<suffix>]_defacemask.nii[.gz]
 ```
 
 The term anatomical imaging data pertains to a broad range of MRI applications that provide structural 
@@ -349,6 +349,27 @@ can also be used to make that distinction. At what level of detail to make the
 distinction (e.g. just between RARE and FLASH, or between RARE, FLASH, and
 FLASHsubsampled) remains at the discretion of the researcher.
 
+#### The `echo` entity
+
+### The echo entity 
+
+If the value of `EchoTime` metadata field varies at least once across a collection 
+of anatomical images having a common `grouping suffix`, the use of `echo-<index>`
+key/value pair is REQUIRED. Note that only integers (from 1 to N) are allowed as
+values to this entity for N different `EchoTime` parameter values. The actual 
+`EchoTime` parameter values MUST NOT be explicitly declared by the entity. Instead, 
+the parameter values are stored in sidecar json files and indexed by the `echo` entity
+in ascending order. For example: 
+
+```
+sub-01_echo-1_MEGRE.nii.gz
+sub-01_echo-1_MEGRE.json   (`EchoTime` = 0.0005)
+sub-01_echo-2_MEGRE.nii.gz 
+sub-01_echo-2_MEGRE.json   (`EchoTime` = 0.0015)
+sub-01_echo-3_MEGRE.nii.gz
+sub-01_echo-3_MEGRE.json   (`EchoTime` = 0.0025)
+```
+
 #### The `ce` entity
 
 Similarly the OPTIONAL `ce-<label>` key/value can be used to distinguish

From 3c7d408387e1889d84019d0532a01cb6650ef23b Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 17:02:37 -0400
Subject: [PATCH 40/76] [ADD] Entitiy for FlipAngle

---
 .../01-magnetic-resonance-imaging-data.md     | 25 +++++++++++++++----
 1 file changed, 20 insertions(+), 5 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 8a8772bc86..874dab02ef 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
@@ -124,8 +124,8 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     anat/
-        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_echo-<index>][_ce-<label>][_rec-<label>][_run-<index>]_<suffix>.nii[.gz]
-        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_echo-<index>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<suffix>]_defacemask.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_echo-<index>][_fa-<index>][_ce-<label>][_rec-<label>][_run-<index>]_<suffix>.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_echo-<index>][_fa-<index>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<suffix>]_defacemask.nii[.gz]
 ```
 
 The term anatomical imaging data pertains to a broad range of MRI applications that provide structural 
@@ -349,9 +349,7 @@ can also be used to make that distinction. At what level of detail to make the
 distinction (e.g. just between RARE and FLASH, or between RARE, FLASH, and
 FLASHsubsampled) remains at the discretion of the researcher.
 
-#### The `echo` entity
-
-### The echo entity 
+#### The echo entity 
 
 If the value of `EchoTime` metadata field varies at least once across a collection 
 of anatomical images having a common `grouping suffix`, the use of `echo-<index>`
@@ -370,6 +368,23 @@ sub-01_echo-3_MEGRE.nii.gz
 sub-01_echo-3_MEGRE.json   (`EchoTime` = 0.0025)
 ```
 
+#### The fa entity 
+
+If the value of `FlipAngle` metadata field varies at least once across a collection 
+of anatomical images having a common `grouping suffix`, the use of `fa-<index>`
+key/value pair is REQUIRED. Note that only integers from 1 to N are allowed as
+values to this entity for N different `FlipAngle` parameter values. The actual 
+`FlipAngle` parameter values MUST NOT be explicitly declared by the entity. Instead,
+the parameter values are stored in sidecar json files and indexed by the `fa` entity
+in ascending order. For example:
+
+```
+sub-01_fa-1_VFA.nii.gz 
+sub-01_fa-1_VFA.json   (`FlipAngle` = 5)
+sub-01_fa-2_VFA.nii.gz 
+sub-01_fa-2_VFA.json   (`FlipAngle` = 25)
+```
+
 #### The `ce` entity
 
 Similarly the OPTIONAL `ce-<label>` key/value can be used to distinguish

From f34fdd8a00b3210afe8307fa2a14fef22dcaf8d6 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 17:08:08 -0400
Subject: [PATCH 41/76] [ADD] inv entity

---
 .../01-magnetic-resonance-imaging-data.md     | 19 +++++++++++++++++++
 1 file changed, 19 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 874dab02ef..30115bceff 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
@@ -385,6 +385,25 @@ sub-01_fa-2_VFA.nii.gz
 sub-01_fa-2_VFA.json   (`FlipAngle` = 25)
 ```
 
+#### The `inv` entity 
+
+If the value of `InversionTime` metadata field varies at least once across a 
+collection of anatomical images having a common `grouping suffix`, the use of 
+`inv-<index>` key/value pair is REQUIRED. Note that only integers from 1 to N 
+are allowed as values to this entity for N different `InversionTime` parameter 
+values. The actual `InversionTime` parameter values MUST NOT be explicitly declared 
+by the entity. Instead, the parameter values are stored in sidecar json files and 
+indexed by the `inv` entity in ascending order. For example: 
+
+```
+sub-01_inv-1_IRT1.nii.gz
+sub-01_inv-1_IRT1.json     (`InversionTime` = 0.0050)
+sub-01_inv-2_IRT1.nii.gz
+sub-01_inv-2_IRT1.json     (`InversionTime` = 0.0100)
+sub-01_inv-3_IRT1.nii.gz
+sub-01_inv-4_IRT1.json     (`InversionTime` = 0.0150)
+```
+
 #### The `ce` entity
 
 Similarly the OPTIONAL `ce-<label>` key/value can be used to distinguish

From 7a0cc024adea0e368df2b3525566d400a891a4e6 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 17:10:55 -0400
Subject: [PATCH 42/76] [ADD]  to template

---
 .../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 30115bceff..3da30585c8 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
@@ -124,8 +124,8 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     anat/
-        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_echo-<index>][_fa-<index>][_ce-<label>][_rec-<label>][_run-<index>]_<suffix>.nii[.gz]
-        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_echo-<index>][_fa-<index>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<suffix>]_defacemask.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_echo-<index>][_fa-<index>][_inv-<index>][_ce-<label>][_rec-<label>][_run-<index>]_<suffix>.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_echo-<index>][_fa-<index>][_inv-<index>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<suffix>]_defacemask.nii[.gz]
 ```
 
 The term anatomical imaging data pertains to a broad range of MRI applications that provide structural 

From ac788c737ee9ef1101351dd4188886da0f66a0e2 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 17 May 2020 17:14:23 -0400
Subject: [PATCH 43/76] [ADD] mt entity

---
 .../01-magnetic-resonance-imaging-data.md     | 22 +++++++++++++++----
 1 file changed, 18 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 874dab02ef..4babe04b10 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
@@ -124,8 +124,8 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     anat/
-        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_echo-<index>][_fa-<index>][_ce-<label>][_rec-<label>][_run-<index>]_<suffix>.nii[.gz]
-        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_echo-<index>][_fa-<index>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<suffix>]_defacemask.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_echo-<index>][_fa-<index>][_mt-<on/off>][_ce-<label>][_rec-<label>][_run-<index>]_<suffix>.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_echo-<index>][_fa-<index>][_mt-<on/off>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<suffix>]_defacemask.nii[.gz]
 ```
 
 The term anatomical imaging data pertains to a broad range of MRI applications that provide structural 
@@ -349,7 +349,7 @@ can also be used to make that distinction. At what level of detail to make the
 distinction (e.g. just between RARE and FLASH, or between RARE, FLASH, and
 FLASHsubsampled) remains at the discretion of the researcher.
 
-#### The echo entity 
+#### The `echo` entity 
 
 If the value of `EchoTime` metadata field varies at least once across a collection 
 of anatomical images having a common `grouping suffix`, the use of `echo-<index>`
@@ -368,7 +368,7 @@ sub-01_echo-3_MEGRE.nii.gz
 sub-01_echo-3_MEGRE.json   (`EchoTime` = 0.0025)
 ```
 
-#### The fa entity 
+#### The `fa` entity 
 
 If the value of `FlipAngle` metadata field varies at least once across a collection 
 of anatomical images having a common `grouping suffix`, the use of `fa-<index>`
@@ -385,6 +385,20 @@ sub-01_fa-2_VFA.nii.gz
 sub-01_fa-2_VFA.json   (`FlipAngle` = 25)
 ```
 
+#### The `mt` entity 
+
+If a collection of anatomical images having a common `grouping suffix` includes
+at least one scan in which a magnetization transfer pulse is applied, the 
+`mt-<on/off>` key/value pair MUST BE used. The value of this entity can be either 
+`on` or `off` (in lowercase), as determined by the `MTState` metadata. For example: 
+
+```
+sub-01_mt-on_MTR.nii.gz
+sub-01_mt-on_MTR.json      (`MTState` = On)
+sub-01_mt-off_MTR.nii.gz
+sub-01_mt-off_MTR.json     (`MTState` = Off)
+```
+
 #### The `ce` entity
 
 Similarly the OPTIONAL `ce-<label>` key/value can be used to distinguish

From d7df8668571d6d9b827d01b83dde305ace20cd71 Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Mon, 18 May 2020 12:50:00 +0200
Subject: [PATCH 44/76] Make reference in fMRI part about echoTime in
 structural part

---
 .../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 73bf0d02b9..8d33c94696 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
@@ -536,7 +536,8 @@ sub-01/
 
 Please note that the `<index>` denotes the number/index (in a form of an
 integer) of the echo not the echo time value which needs to be stored in the
-field EchoTime of the separate JSON file.
+field EchoTime of the separate JSON file (see also 
+[here](01-magnetic-resonance-imaging-data.md#the-echo-entity)).
 
 Some meta information about the acquisition MUST be provided in an additional
 JSON file.

From c3dc583e883075764f5b0d969feea5f98a5b83e7 Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Mon, 18 May 2020 13:19:25 +0200
Subject: [PATCH 45/76] Dissociate between B0 and B1 fieldmaps

---
 .../01-magnetic-resonance-imaging-data.md     | 19 +++++++++++++++----
 1 file changed, 15 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 73bf0d02b9..3ca3a66d40 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
@@ -703,6 +703,17 @@ JSON example:
 
 ### Fieldmap data
 
+Both B0 (static magnetic field strength pattern), B1+ (transmit field pattern), and
+B1- (receive field pattern) maps can be useful in post-processing raw functional and
+anatomical data.
+
+B0 maps are primarily used to correct for spatial distortions in functional data
+acquired with EPI sequences.
+
+B1+ and B1- maps are mostly used in anatomical imaging, especially when applying
+quantitative MRI (qMRI or hMRI) techniques.
+
+#### B0 fieldmaps
 Data acquired to correct for B0 inhomogeneities can come in different forms. The
 current version of this standard considers four different scenarios. Please note
 that in all cases fieldmap data can be linked to a specific scan(s) it was
@@ -733,7 +744,7 @@ Multiple fieldmaps can be stored. In such case the `_run-1`, `_run-2` should be
 used. The OPTIONAL `acq-<label>` key/value pair corresponds to a custom label
 the user may use to distinguish different set of parameters.
 
-#### Case 1: Phase difference image and at least one magnitude image
+##### Case 1: Phase difference image and at least one magnitude image
 
 Template:
 
@@ -768,7 +779,7 @@ the shorter echo time and `EchoTime2` to the longer echo time. Similarly
 }
 ```
 
-#### Case 2: Two phase images and two magnitude images
+##### Case 2: Two phase images and two magnitude images
 
 Template:
 
@@ -794,7 +805,7 @@ corresponding `EchoTime` values. For example:
 }
 ```
 
-#### Case 3: A real fieldmap image
+##### Case 3: A real fieldmap image
 
 Template:
 
@@ -818,7 +829,7 @@ the fieldmap. The possible options are: `Hz`, `rad/s`, or `Tesla`. For example:
 }
 ```
 
-#### Case 4: Multiple phase encoded directions ("pepolar")
+##### Case 4: Multiple phase encoded directions ("pepolar")
 
 Template:
 

From 217f2ad8a7d6b097d670cf7e751331bae5766184 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Tue, 19 May 2020 07:57:54 -0400
Subject: [PATCH 46/76] [ADD] S0map

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

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 3da30585c8..3b8016ebda 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
@@ -309,6 +309,7 @@ expand or to modify the following table.
 | Myelin water fraction map                              | MWFmap    | Parametric   | In percentage (%). MWF maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`                                                                                                                                          |
 | Combined PD/T2 map                                     | PDT2map   | Parametric   | In arbitrary units (a.u.). Combined PD/T2 maps are REQUIRED to use this suffix irrespective of the method they are related to. N/A                                                                                                                                                   |
 | RF transmit field map                                  | B1plusmap | Parametric   | In arbitrary units (a.u.). Radio frequency (RF) transmit field maps are REQUIRED to use this suffix irrespective of the method they are related to. For further details please see the fieldmap data section.  _Can be generated from_: `B1DAM`                                                                      |
+| Observed signal amplitude map                                | S0map | Parametric   | In arbitrary units (a.u.). For a multi-echo sequence, S0 maps index the baseline signal before exponential (T2*) 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 REQUIRED to use this suffix irrespective of the method they are related to. _Associated suffixes:_ T2starmap.       |
 
 Quantitative maps can be obtained right off the scanner or by processing files
 belonging to a `grouped scan collection`. Regardless of the method they are

From 65ea2f618f9a5d3a7a6b25577901c6ff5a68b974 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Tue, 26 May 2020 07:36:41 -0400
Subject: [PATCH 47/76] Cleanup RF map text

---
 .../01-magnetic-resonance-imaging-data.md     |  4 +--
 src/99-appendices/10-qmri.md                  | 34 ++++++++-----------
 2 files changed, 17 insertions(+), 21 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 f8b466eee9..4c0a13b6ee 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
@@ -263,7 +263,6 @@ A change to the specification is REQUIRED to expand or to modify the following t
 | Magnetization transfer ratio               | MTR     | Grouping | Parametrically linked anatomical images for calculating a semi-quantitative magnetization transfer ratio map. _Associated output suffixes_: MTRmap                                                                                                                                                                                                                                                                                                                                                                                 |
 | Magnetization transfer saturation          | MTS     | Grouping | Parametrically linked anatomical images for calculating 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)). _Associated output suffixes_: T1map, MTsat                                                                                                                                                                                               |
 | Multi-parametric mapping                   | MPM     | Grouping | Parametrically linked anatomical images for multiparametric mapping (a.k.a hMRI). The MPM approaches 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.,_Associated output suffixes_:R1map, R2starmap, MTsat, PDmap, T1map, T2starmap                                               |
-| Double-angle B1 mapping                    | B1DAM   | Grouping | Parametrically linked anatomical images for RF transmit field (B1 plus) mapping ([Insko and Bolinger 1993](https://www.sciencedirect.com/science/article/abs/pii/S1064185883711332)). Double angle method is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation angles. Common sequence types for this application include spin echo and echo planar imaging. _Associated output suffixes_: B1plusmap                                                                                                                                                      |
 
 For example:
 
@@ -308,7 +307,8 @@ expand or to modify the following table.
 | Longutidunal relaxation in rotating frame (T1 rho) map | T1rho     | Parametric   | In seconds (s). T1-rho maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ N/A                                                                                                                                             |
 | Myelin water fraction map                              | MWFmap    | Parametric   | In percentage (%). MWF maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`                                                                                                                                          |
 | Combined PD/T2 map                                     | PDT2map   | Parametric   | In arbitrary units (a.u.). Combined PD/T2 maps are REQUIRED to use this suffix irrespective of the method they are related to. N/A                                                                                                                                                   |
-| RF transmit field map                                  | B1plusmap | Parametric   | In arbitrary units (a.u.). Radio frequency (RF) transmit field maps are REQUIRED to use this suffix irrespective of the method they are related to. For further details please see the fieldmap data section.  _Can be generated from_: `B1DAM`                                                                      |
+| RF transmit field map                                  | B1plusmap | Parametric   | 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. Please see the [qMRI appendix]() for associated inputs and further details                                                                     |
+| RF receive sensitivity map                                  | B1minusmap | Parametric   | 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. Please see the [qMRI appendix]() for associated inputs and further details                                                                     |
 | Observed signal amplitude map                                | S0map | Parametric   | In arbitrary units (a.u.). For a multi-echo sequence, S0 maps index the baseline signal before exponential (T2*) 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 REQUIRED to use this suffix irrespective of the method they are related to. _Associated suffixes:_ T2starmap.       |
 
 Quantitative maps can be obtained right off the scanner or by processing files
diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index 76eb1ef59f..62f623e6f9 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -126,24 +126,20 @@ BIDS-apps. For example:
  |               ├── sub-01_T1map.json   ───────┐ | Y
  |               ├── sub-01_MTsat.nii.gz ─────┐ | | M
  |               └── sub-01_MTsat.json   ───┐ | | | L 
- ├── sub-01/                                | | | | I
- |   ├── anat/                              | | | | N
- |   |   ├── sub-01_T1w.nii.gz              | | | | K
- |   |   ├── sub-01_T1w.json                | | | | 
- |   |   ├── sub-01_fa-1_mt-on_MTS.nii.gz   | | | | T
- |   |   ├── sub-01_fa-1_mt-on_MTS.json     | | | | O 
- |   |   ├── sub-01_fa-1_mt-off_MTS.nii.gz  | | | | 
- |   |   ├── sub-01_fa-1_mt-off_MTS.json    | | | | A
- |   |   ├── sub-01_fa-2_mt-off_MTS.nii.gz  | | | | N
- |   |   ├── sub-01_fa-2_mt-off_MTS.json    | | | | A
- |   |   ├── sub-01_T1map.nii.gz ◀───────────├─├─├─┘ T
- |   |   ├── sub-01_T1map.json   ◀───────────├─├─┘   
- |   |   ├── sub-01_MTsat.nii.gz ◀───────────├─┘     
- |   |   └── sub-01_MTsat.json   ◀───────────┘         
- |   |
- |   └──func/..
- |
- └── sub-#N/..
+ └── sub-01/                                | | | | I
+     └── anat/                              | | | | N
+         ├── sub-01_T1w.nii.gz              | | | | K
+         ├── sub-01_T1w.json                | | | | 
+         ├── sub-01_fa-1_mt-on_MTS.nii.gz   | | | | T
+         ├── sub-01_fa-1_mt-on_MTS.json     | | | | O 
+         ├── sub-01_fa-1_mt-off_MTS.nii.gz  | | | | 
+         ├── sub-01_fa-1_mt-off_MTS.json    | | | | A
+         ├── sub-01_fa-2_mt-off_MTS.nii.gz  | | | | N
+         ├── sub-01_fa-2_mt-off_MTS.json    | | | | A
+         ├── sub-01_T1map.nii.gz ◀──────────├─├─├─┘ T
+         ├── sub-01_T1map.json   ◀──────────├─├─┘   
+         ├── sub-01_MTsat.nii.gz ◀──────────├─┘
+         └── sub-01_MTsat.json   ◀──────────┘ 
 ```
 
 In the example above, outputs of the `MTS` that are placed under the `derivatives`
@@ -229,4 +225,4 @@ sub-01_T1map.json
 “EstimationSoftwareVersion”: “2.3.0”,
 “EstimationSoftwareEnv”: “Ubuntu 16.04”
 }
-```
+```
\ No newline at end of file

From 39b9c1d6690d0844d14d3914f658b45a3c373d5d Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Tue, 26 May 2020 07:38:11 -0400
Subject: [PATCH 48/76] [ADD] RF field maps

---
 src/99-appendices/10-qmri.md | 166 +++++++++++++++++++++++++++++++++++
 1 file changed, 166 insertions(+)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index 62f623e6f9..5c23e573fd 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -225,4 +225,170 @@ sub-01_T1map.json
 “EstimationSoftwareVersion”: “2.3.0”,
 “EstimationSoftwareEnv”: “Ubuntu 16.04”
 }
+```
+
+# Radiofrequency (RF) field mapping 
+
+Most qMRI methods are susceptible to the nonuniformities in the transmit (B1<sup>+</sup>) and/or receive (B1<sup>-</sup>) radiofrequency (RF) fields. Various (acquisition based)
+methods are available to derive maps of spatial variations in the B1<sup>+</sup> and B1<sup>-</sup> 
+fields. These maps are commonly used for the correction of qMRI estimation errors 
+arising from the imperfections in the respective RF field.
+
+An approach similar to that used in anatomical MR images to group a set of input images intended
+for qMRI application (`grouping suffix`) is applied for the inputs of B1<sup>+</sup> and B1<sup>-</sup> RF field mapping. Note that these images do not convey substantial
+structural information by design. Therefore, both inputs and outputs of RF field
+maps are stored in the `fmap` folder.
+
+## Grouping suffixes for RF field mapping 
+
+| Name                                       | Suffix  | Type     | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
+|--------------------------------------------|---------|----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| Double-angle B1<sup>+</sup> mapping                    | TB1DAM   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Insko and Bolinger 1993](https://www.sciencedirect.com/science/article/abs/pii/S1064185883711332)). Double angle method 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. _Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
+| B1<sup>+</sup> mapping with 3D EPI            | TB1EPI   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)). This method 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. _Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
+| Actual Flip Ange Imaging (AFI)             | TB1AFI   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Yarnykh 2007](https://dx.doi.org/10.1002/mrm.21120)). This method calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence. _Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
+| Siemens `tfl_b1_map`             | TB1TFL   | RF Grouping | Groups images 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._Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
+| Siemens `rf_map`             | TB1RFM   | RF Grouping | Groups images acquired using `rf_map` product sequence by Siemens, using a method combining SE and STE images with EPI readout similar to that by ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)). The sequence generates one ~anatomical image and one scaled flip angle map. _Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
+| B1<sup>-</sup> field correction          | RB1COR   | RF Grouping | Groups 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). _Associated output suffixes_: `B1minusmap`                                                                                                                                                      |
+
+## Entity specifications for RF field mapping grouping suffixes
+
+### `TB1DAM` 
+
+The `fa` entity MUST be used to distinguish images with this suffix: 
+
+```
+└── sub-01/
+     └── fmap/
+         ├── sub-01_fa-1_TB1DAM.nii.gz
+         ├── sub-01_fa-1_TB1DAM.json
+         ├── sub-01_fa-2_TB1DAM.nii.gz
+         └── sub-01_fa-2_TB1DAM.json
+```
+
+### `TB1EPI`
+
+The `fa` and `echo` entities MUST be used to distinguish images with this suffix.
+The use of `fa` follows the default convention. However, this suffix defines a
+specific use case for the `echo` entity:
+
+At each `FlipAngle`, the `TB1EPI` suffix lists two images acquired at two echo times.
+However, the second echo in this method is generated in a different fashion compared 
+to the `MESE`. The first echo is a typical spin echo (SE), whereas the second
+echo is a stimulated echo (STE) that is not generated by an inversion pulse. 
+
+To properly identify constituents of this particular method, values of the `echo`
+entity MUST index the images as follows:  
+
+|`echo-1`|`echo-2`|
+|:--|:----|
+|Lower `EchoTime` | Higher `EchoTime`                  |
+|Spin Echo (SE) image|Stimulated Echo (STE) image|
+
+
+```
+└── sub-01/
+     └── fmap/
+         ├── sub-01_fa-1_echo-1_TB1EPI.nii.gz (SE)
+         ├── sub-01_fa-1_echo-1_TB1EPI.nii.gz
+         ├── sub-01_fa-1_echo-2_TB1EPI.nii.gz (STE)
+         ├── sub-01_fa-1_echo-2_TB1EPI.nii.gz
+         ├── sub-01_fa-2_echo-1_TB1EPI.nii.gz (SE)
+         ├── sub-01_fa-2_echo-1_TB1EPI.nii.gz
+         ├── sub-01_fa-2_echo-2_TB1EPI.nii.gz (STE)
+         └── sub-01_fa-2_echo-2_TB1EPI.nii.gz
+```
+
+### `TB1AFI`
+
+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, the  `acq` entity SHOULD be used with `tr1` (lower TR) 
+and `tr2` (higher TR) values for this particular use case: 
+
+```
+└── 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`
+
+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 images and the second output is a scaled flip angle map.
+The `acq` entity SHOULD be used with `anat` and `sfamap` (scaled fa map) values 
+for these particular use cases:
+
+```
+└── sub-01/
+     └── fmap/
+         ├── sub-01_acq-anat_TB1TFL.nii.gz 
+         ├── sub-01_acq-anat_TB1TFL.json
+         ├── sub-01_acq-sfamap_TB1TFL.nii.gz
+         └── sub-01_acq-sfamap_TB1TFL.json
+```
+
+The example above applies to the `TB1RFM` suffix as well. 
+
+### `RB1COR`
+
+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. In this respect, the data pair answers 
+to the description of the `run` entity.
+
+To properly identify constituents of this particular method, values of the `run`
+entity MUST index the images as follows:  
+
+|`run-1`|`run-2`|
+|:--|:----|
+|Body coil | Head coil|
+
+
+```
+└── sub-01/
+     └── fmap/
+         ├── sub-01_run-1_RB1COR.nii.gz (Body coil)
+         ├── sub-01_run-1_RB1COR.json
+         ├── sub-01_run-2_RB1COR.nii.gz (Head coil)
+         └── sub-01_run-2_RB1COR.json
+```
+
+## Where to place RF field maps? 
+
+**If the RF field map is generated using an open-source software:**
+
+RF field maps SHOULD be stored in the `derivatives` folder, but MAY
+be symbolic linked to the corresponding raw data directory to facilitate the
+easy use of these images as input to processing workflows implemented as
+BIDS-apps. For example:
+
+```diff
+ ds-example/
+ ├── derivatives/
+ |   └── qMRI-software/
+ |       └── sub-01/
+ |           └── fmap/
+ |               ├── sub-01_acq-PDw_B1minusmap.nii.gz    ─────────┐ 
+ |               ├── sub-01_acq-PDw_B1minusmap.json      ───────┐ | 
+ |               ├── sub-01_B1plusmap.nii.gz             ─────┐ | | 
+ |               └── sub-01_B1plusmap.json               ───┐ | | | 
+ └── sub-01/                                                | | | | S
+     └── fmap/                                              | | | | Y
+         ├── sub-01_acq-PDw_run-1_RB1COR.nii.gz             | | | | M
+         ├── sub-01_acq-PDw_run-1_RB1COR.json               | | | | L
+         ├── sub-01_acq-PDw_run-2_RB1COR.nii.gz             | | | | I
+         ├── sub-01_acq-PDw_run-2_RB1COR.json               | | | | N
+         ├── sub-01_fa-1_TB1DAM.nii.gz                      | | | | K
+         ├── sub-01_fa-1_TB1DAM.json                        | | | | 
+         ├── sub-01_fa-2_TB1DAM.nii.gz                      | | | | T
+         ├── sub-01_fa-2_TB1DAM.json                        | | | | O
+         ├── sub-01_acq-PDw_B1minusmap.nii.gz  ◀────────────├─├─├─┘
+         ├── sub-01_acq-PDw_B1minusmap.json    ◀────────────├─├─┘
+         ├── sub-01_B1plusmap.nii.gz           ◀────────────├─┘
+         └── sub-01_B1plusmap.json             ◀────────────┘
 ```
\ No newline at end of file

From ee586a68928f13fddd20ac64f944b5fd55ade8d7 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 27 May 2020 05:01:10 -0400
Subject: [PATCH 49/76] [FIX] Table

---
 src/99-appendices/10-qmri.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index 5c23e573fd..5ecf529f64 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -289,13 +289,13 @@ entity MUST index the images as follows:
 └── sub-01/
      └── fmap/
          ├── sub-01_fa-1_echo-1_TB1EPI.nii.gz (SE)
-         ├── 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 (STE)
-         ├── 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 (SE)
-         ├── 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 (STE)
-         └── sub-01_fa-2_echo-2_TB1EPI.nii.gz
+         └── sub-01_fa-2_echo-2_TB1EPI.json
 ```
 
 ### `TB1AFI`

From ca60c07b5bd3197086cff06290b3237ec29673e5 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 27 May 2020 05:11:30 -0400
Subject: [PATCH 50/76] [ADD] Reference to the apendix

---
 .../01-magnetic-resonance-imaging-data.md         | 15 ++++++++-------
 1 file changed, 8 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 4c0a13b6ee..b35536d0b6 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
@@ -307,8 +307,8 @@ expand or to modify the following table.
 | Longutidunal relaxation in rotating frame (T1 rho) map | T1rho     | Parametric   | In seconds (s). T1-rho maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ N/A                                                                                                                                             |
 | Myelin water fraction map                              | MWFmap    | Parametric   | In percentage (%). MWF maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`                                                                                                                                          |
 | Combined PD/T2 map                                     | PDT2map   | Parametric   | In arbitrary units (a.u.). Combined PD/T2 maps are REQUIRED to use this suffix irrespective of the method they are related to. N/A                                                                                                                                                   |
-| RF transmit field map                                  | B1plusmap | Parametric   | 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. Please see the [qMRI appendix]() for associated inputs and further details                                                                     |
-| RF receive sensitivity map                                  | B1minusmap | Parametric   | 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. Please see the [qMRI appendix]() for associated inputs and further details                                                                     |
+| RF transmit field map                                  | B1plusmap | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/10-qmri.md) for associated inputs and further details                                                                     |
+| RF receive sensitivity map                                  | B1minusmap | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/10-qmri.md) for associated inputs and further details                                                                     |
 | Observed signal amplitude map                                | S0map | Parametric   | In arbitrary units (a.u.). For a multi-echo sequence, S0 maps index the baseline signal before exponential (T2*) 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 REQUIRED to use this suffix irrespective of the method they are related to. _Associated suffixes:_ T2starmap.       |
 
 Quantitative maps can be obtained right off the scanner or by processing files
@@ -705,15 +705,16 @@ JSON example:
 
 ### Fieldmap data
 
-Both B0 (static magnetic field strength pattern), B1+ (transmit field pattern), and
-B1- (receive field pattern) maps can be useful in post-processing raw functional and
+All three of B0 (static magnetic field strength pattern), B1<sup>+</sup> (transmit field pattern), and
+B1<sup>-</sup> (receive field pattern) maps can be useful in post-processing raw functional and
 anatomical data.
 
 B0 maps are primarily used to correct for spatial distortions in functional data
 acquired with EPI sequences.
 
-B1+ and B1- maps are mostly used in anatomical imaging, especially when applying
-quantitative MRI (qMRI or hMRI) techniques.
+B1<sup>+</sup> and B1<sup>+</sup>  maps are mostly used in anatomical imaging, especially
+in quantitative MRI applications. Further information about these radiofrequency (RF)
+field maps are available in the [qMRI appendix](../99-appendices/10-qmri.md).
 
 #### B0 fieldmaps
 Data acquired to correct for B0 inhomogeneities can come in different forms. The
@@ -869,4 +870,4 @@ encoding directions) of the corresponding sequence. Please rely only on the JSON
 file to obtain scanning parameters. \_epi files can be a 3D or 4D - in the
 latter case all timepoints share the same scanning parameters. To indicate which
 run is intended to be used with which functional or diffusion scan the
-IntendedFor field in the JSON file should be used.
+IntendedFor field in the JSON file should be used.
\ No newline at end of file

From 8d7efc354fe447270140e246fce4dec27c60beae Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 27 May 2020 05:38:15 -0400
Subject: [PATCH 51/76] [CHANGE] Entity use for RB1COR

---
 src/99-appendices/10-qmri.md | 63 +++++++++++++++++++++++-------------
 1 file changed, 41 insertions(+), 22 deletions(-)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index 5ecf529f64..e0b7f61a73 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -303,8 +303,17 @@ entity MUST index the images as follows:
 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, the  `acq` entity SHOULD be used with `tr1` (lower TR) 
-and `tr2` (higher TR) values for this particular use case: 
+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/
@@ -320,16 +329,24 @@ and `tr2` (higher TR) values for this particular use case:
 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 images and the second output is a scaled flip angle map.
-The `acq` entity SHOULD be used with `anat` and `sfamap` (scaled fa map) values 
-for these particular use cases:
+
+To properly identify constituents of this particular method, 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-sfamap_TB1TFL.nii.gz
-         └── sub-01_acq-sfamap_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. 
@@ -338,24 +355,26 @@ The example above applies to the `TB1RFM` suffix as well.
 
 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. In this respect, the data pair answers 
-to the description of the `run` entity.
+with identical acquisition parameters.
 
-To properly identify constituents of this particular method, values of the `run`
-entity MUST index the images as follows:  
-
-|`run-1`|`run-2`|
-|:--|:----|
-|Body coil | Head coil|
+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_run-1_RB1COR.nii.gz (Body coil)
-         ├── sub-01_run-1_RB1COR.json
-         ├── sub-01_run-2_RB1COR.nii.gz (Head coil)
-         └── sub-01_run-2_RB1COR.json
+         ├── 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
 ```
 
 ## Where to place RF field maps? 
@@ -379,10 +398,10 @@ BIDS-apps. For example:
  |               └── sub-01_B1plusmap.json               ───┐ | | | 
  └── sub-01/                                                | | | | S
      └── fmap/                                              | | | | Y
-         ├── sub-01_acq-PDw_run-1_RB1COR.nii.gz             | | | | M
-         ├── sub-01_acq-PDw_run-1_RB1COR.json               | | | | L
-         ├── sub-01_acq-PDw_run-2_RB1COR.nii.gz             | | | | I
-         ├── sub-01_acq-PDw_run-2_RB1COR.json               | | | | N
+         ├── sub-01_acq-bodyPDw_RB1COR.nii.gz               | | | | M
+         ├── sub-01_acq-bodyPDw_RB1COR.json                 | | | | L
+         ├── sub-01_acq-headPDw_RB1COR.nii.gz               | | | | I
+         ├── sub-01_acq-headPDw_RB1COR.json                 | | | | N
          ├── sub-01_fa-1_TB1DAM.nii.gz                      | | | | K
          ├── sub-01_fa-1_TB1DAM.json                        | | | | 
          ├── sub-01_fa-2_TB1DAM.nii.gz                      | | | | T

From c5860cb55073998a31f4ea2809e9c54fd1b88df6 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Wed, 27 May 2020 05:39:45 -0400
Subject: [PATCH 52/76] [MINOR] 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 b35536d0b6..aae8171c37 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
@@ -712,7 +712,7 @@ anatomical data.
 B0 maps are primarily used to correct for spatial distortions in functional data
 acquired with EPI sequences.
 
-B1<sup>+</sup> and B1<sup>+</sup>  maps are mostly used in anatomical imaging, especially
+B1<sup>+</sup> and B1<sup>-</sup>  maps are mostly used in anatomical imaging, especially
 in quantitative MRI applications. Further information about these radiofrequency (RF)
 field maps are available in the [qMRI appendix](../99-appendices/10-qmri.md).
 

From 887e2f47ffe0c48f7a6adb8aa7cd04c1ee281411 Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Fri, 5 Jun 2020 14:15:20 +0200
Subject: [PATCH 53/76] Added  to qmaps

---
 .../01-magnetic-resonance-imaging-data.md                       | 2 ++
 1 file changed, 2 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 aae8171c37..68eb18c084 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
@@ -310,6 +310,8 @@ expand or to modify the following table.
 | RF transmit field map                                  | B1plusmap | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/10-qmri.md) for associated inputs and further details                                                                     |
 | RF receive sensitivity map                                  | B1minusmap | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/10-qmri.md) for associated inputs and further details                                                                     |
 | Observed signal amplitude map                                | S0map | Parametric   | In arbitrary units (a.u.). For a multi-echo sequence, S0 maps index the baseline signal before exponential (T2*) 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 REQUIRED to use this suffix irrespective of the method they are related to. _Associated suffixes:_ T2starmap.       |
+| Quantitative susceptibility map (QSM)                   | Chimap | Parametric   | In parts per million (ppm). QSM allows for determining the bulk magnetic susceptibility distribution of 
+tissue (Chi) and are usually constructed from the phase images of GRE sequences. The resulting maps are quantitative and are reconstructed by solving the magnetic field to susceptibility source inverse problem ([Wang & Liu, 2014](https://onlinelibrary.wiley.com/doi/10.1002/mrm.25358)). |
 
 Quantitative maps can be obtained right off the scanner or by processing files
 belonging to a `grouped scan collection`. Regardless of the method they are

From d89c8cae22f82ff214c22893dab6ae34c3030e4f Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Fri, 5 Jun 2020 14:18:42 +0200
Subject: [PATCH 54/76] Some rewording

---
 .../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 68eb18c084..bbc54b6141 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
@@ -311,7 +311,7 @@ expand or to modify the following table.
 | RF receive sensitivity map                                  | B1minusmap | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/10-qmri.md) for associated inputs and further details                                                                     |
 | Observed signal amplitude map                                | S0map | Parametric   | In arbitrary units (a.u.). For a multi-echo sequence, S0 maps index the baseline signal before exponential (T2*) 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 REQUIRED to use this suffix irrespective of the method they are related to. _Associated suffixes:_ T2starmap.       |
 | Quantitative susceptibility map (QSM)                   | Chimap | Parametric   | In parts per million (ppm). QSM allows for determining the bulk magnetic susceptibility distribution of 
-tissue (Chi) and are usually constructed from the phase images of GRE sequences. The resulting maps are quantitative and are reconstructed by solving the magnetic field to susceptibility source inverse problem ([Wang & Liu, 2014](https://onlinelibrary.wiley.com/doi/10.1002/mrm.25358)). |
+tissue (Chi). Chi-maps are usually constructed from the phase images of GRE sequences. Chi-maps are quantitative and are reconstructed by solving the magnetic field to susceptibility source inverse problem ([Wang & Liu, 2014](https://onlinelibrary.wiley.com/doi/10.1002/mrm.25358)). |
 
 Quantitative maps can be obtained right off the scanner or by processing files
 belonging to a `grouped scan collection`. Regardless of the method they are

From 05a7fa5491ecf99825697eca74309d0cff57c6e3 Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Mon, 8 Jun 2020 10:28:28 +0200
Subject: [PATCH 55/76] Implemented @agahkarakuzu's wording suggestion

---
 .../01-magnetic-resonance-imaging-data.md                      | 3 +--
 1 file changed, 1 insertion(+), 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 bbc54b6141..7cc734f434 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
@@ -310,8 +310,7 @@ expand or to modify the following table.
 | RF transmit field map                                  | B1plusmap | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/10-qmri.md) for associated inputs and further details                                                                     |
 | RF receive sensitivity map                                  | B1minusmap | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/10-qmri.md) for associated inputs and further details                                                                     |
 | Observed signal amplitude map                                | S0map | Parametric   | In arbitrary units (a.u.). For a multi-echo sequence, S0 maps index the baseline signal before exponential (T2*) 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 REQUIRED to use this suffix irrespective of the method they are related to. _Associated suffixes:_ T2starmap.       |
-| Quantitative susceptibility map (QSM)                   | Chimap | Parametric   | In parts per million (ppm). QSM allows for determining the bulk magnetic susceptibility distribution of 
-tissue (Chi). Chi-maps are usually constructed from the phase images of GRE sequences. Chi-maps are quantitative and are reconstructed by solving the magnetic field to susceptibility source inverse problem ([Wang & Liu, 2014](https://onlinelibrary.wiley.com/doi/10.1002/mrm.25358)). |
+| Quantitative susceptibility map (QSM)                   | Chimap | Parametric   | In parts per million (ppm). QSM allows for determining the underlying magnetic susceptibility of tissue (Chi).  Chi-maps are usually constructed from the phase images of GRE sequences. Chi-maps are quantitative and are reconstructed by solving the magnetic field to susceptibility source inverse problem ([Wang & Liu, 2014](https://onlinelibrary.wiley.com/doi/10.1002/mrm.25358)). |
 
 Quantitative maps can be obtained right off the scanner or by processing files
 belonging to a `grouped scan collection`. Regardless of the method they are

From 389c0a9446d2896d616f31604e1512b7d44a093a Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Mon, 8 Jun 2020 10:34:09 +0200
Subject: [PATCH 56/76] Added SA2RAGE B1+-mapping method to qmri appendix

---
 src/99-appendices/10-qmri.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index e0b7f61a73..0f5c1ad3f5 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -248,6 +248,7 @@ maps are stored in the `fmap` folder.
 | Actual Flip Ange Imaging (AFI)             | TB1AFI   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Yarnykh 2007](https://dx.doi.org/10.1002/mrm.21120)). This method calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence. _Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
 | Siemens `tfl_b1_map`             | TB1TFL   | RF Grouping | Groups images 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._Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
 | Siemens `rf_map`             | TB1RFM   | RF Grouping | Groups images acquired using `rf_map` product sequence by Siemens, using a method combining SE and STE images with EPI readout similar to that by ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)). The sequence generates one ~anatomical image and one scaled flip angle map. _Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
+|Saturation‐prepared with 2 rapid Gradient Echoes (SA2RAGE) B1<sup>+</sup> mapping | SA2RAGE | RF Grouping |Groups images for  B1+ field mapping ([Eggenschwiler et al. 2011](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.23145)). SA2RAGE uses a ratio of two saturation recovery images with different time delays, and a simulated look-up table to estimate B1+. This sequence can also be used in conjunction with MP2RAGE T1 mapping to iteratively improve B1+ and T1 map estimation ([Marques & Gruetter 2013](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069294)). Associated output suffixes: B1plusmap                                                                                                                                                     |
 | B1<sup>-</sup> field correction          | RB1COR   | RF Grouping | Groups 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). _Associated output suffixes_: `B1minusmap`                                                                                                                                                      |
 
 ## Entity specifications for RF field mapping grouping suffixes

From cdea8b6ba8e69f26eb47d3f1120e117fa90f2b09 Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Wed, 10 Jun 2020 14:27:01 +0200
Subject: [PATCH 57/76] Some small tweaks

---
 src/99-appendices/10-qmri.md | 43 ++++++++++++++++++++++++++++++------
 1 file changed, 36 insertions(+), 7 deletions(-)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index e0b7f61a73..9191b31db8 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -37,7 +37,7 @@ 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 varying additional scan parameters.
 
-If such inheritance relationship is applicable between an already existing
+If such a inheritance relationship is applicable between an already existing
 `grouping suffix` and a new qMRI application to be included in the specification,
 the inheritor qMRI method MUST be listed in the table below instead of
 introducing a new `grouping suffix`. This approach:
@@ -92,6 +92,35 @@ For a dataset with a `grouping suffix`, the BIDS validation is successful if:
 * provided suffixes are present in the list of available suffixes
 * sidecar JSON files follow the hierarchy defined for `grouping suffix`.
 
+# Introducing a new qMRI grouping suffix
+
+In the future, novel qMRI applications will be introduced that are not yet
+described by the BIDS. If such applications can not be interpreted as a 
+subset of a pre-existing `grouping suffix`,
+a new grouping suffix can be introduced, but should adhere to the following
+principles:
+
+* All grouping suffixes MUST be capitalized.
+* Grouping suffixes MUST attain a clear description of the qMRI application
+that they relate to. Hyperlinks to example applications and/or more detailed
+descriptions are encouraged whenever possible.
+* Unless the pulse sequence is exclusively associated with a specific qMRI
+application (e.g. `MP2RAGE`), sequence names are NOT used as grouping suffixes.
+* If it is possible to derive a qMRI application from an already existing
+grouping suffix by defining a set of logical conditions over the metadata
+fields, the [table of method-specific priority levels](#prioritylevels) and the
+[table of qMRI applications that can be derived from an existing grouping suffix](#varianttable)
+ MUST be expanded instead of introducing a new grouping suffix.
+ Please visit the [JSON content for grouping suffixes](#whichmetadata) 
+ for further details.
+* Please note that if a structural data has the type of grouped scan collection,
+the use of `_suffix` alone cannot distinguish its members from each other,
+failing to identify their roles as inputs to the calculation of qMRI maps.
+Although such images are REQUIRED to be grouped by a proper grouping suffix,
+they are also RECOMMENDED to include at least one of the `acq`, `part`, `echo`,
+`met`, `inv`-key/value-pairs (please visit corresponding sections for details).
+
+
 # Management of the qMRI maps
 
 All qMRI maps are generated following a set of calculations. Unlike conventional 
@@ -99,7 +128,7 @@ MR images, they are not products of an MRI image reconstruction (from k-space da
 to structural images). There are two possible options in the way a qMRI map is obtained: 
 
 1. The qMRI map is calculated at the scanner site through a non-transparent vendor pipeline.
-2. The qMRI map is generated off-site using an open-source software. 
+2. The qMRI map is generated off-site using open-source software. 
 
 ## Where to place qMRI maps? 
 
@@ -109,7 +138,7 @@ Although qMRI maps are derivatives, we cannot relate them to their parent images
 not even be accessible) through a set of calculations in this case. Therefore, such maps obtained
 at the scanner site via non-transparent pipelines are placed at the `/sub-#/anat` directory.
 
-**If the qMRI map is generated using an open-source software:**
+**If the qMRI map is generated using open-source software:**
 
 Quantitative maps SHOULD be stored in the `derivatives` folder, but MAY
 be symbolic linked to the corresponding raw data directory to facilitate the
@@ -146,13 +175,13 @@ In the example above, outputs of the `MTS` that are placed under the `derivative
 folder are symbolic linked to the respective `anat` folder. This way, an
 application can easily pick up a qMRI map along with other anatomical images.
 
-## Which metadata fields should a qMRI map contain? 
+## <a name="whichmetadata">Which metadata fields should a qMRI map contain?</a>
 
 **If the qMRI map is calculated at the scanner site through a non-transparent vendor pipeline:** 
 
 JSON content is confined to the metadata made available by the vendor pipeline.
 
-**If the qMRI map is generated using an open-source software:**
+**If the qMRI map is generated using open-source software:**
 
 JSON file of the qMRI map MUST inherit metadata from its parent images (typically a grouped scan 
 collection) by adhering to the following rules:
@@ -166,7 +195,7 @@ qMRI map **`in array form`**.
  relevant to a given `grouped scan collection`, please see the
 [method-specific priority levels for qMRI metadata](#prioritylevels) above.
 * The JSON file accompanying a qMRI map which is obtained by
-using an open-source software MUST include all the metadata fields listed
+using open-source software MUST include all the metadata fields listed
 in the following table for the sake of provenance.
 
 | Field name                  | Definition                                                     |
@@ -379,7 +408,7 @@ entries:
 
 ## Where to place RF field maps? 
 
-**If the RF field map is generated using an open-source software:**
+**If the RF field map is generated using open-source software:**
 
 RF field maps SHOULD be stored in the `derivatives` folder, but MAY
 be symbolic linked to the corresponding raw data directory to facilitate the

From f79c3d50d8e29790d5aed8dff0c137c16463e848 Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Wed, 10 Jun 2020 14:38:44 +0200
Subject: [PATCH 58/76] Replace B1plusmap with TB1map and B1minusmap with
 RB1map

---
 .../01-magnetic-resonance-imaging-data.md     |  6 ++--
 src/99-appendices/10-qmri.md                  | 32 +++++++++----------
 2 files changed, 19 insertions(+), 19 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 aae8171c37..d992dbb091 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
@@ -307,8 +307,8 @@ expand or to modify the following table.
 | Longutidunal relaxation in rotating frame (T1 rho) map | T1rho     | Parametric   | In seconds (s). T1-rho maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ N/A                                                                                                                                             |
 | Myelin water fraction map                              | MWFmap    | Parametric   | In percentage (%). MWF maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`                                                                                                                                          |
 | Combined PD/T2 map                                     | PDT2map   | Parametric   | In arbitrary units (a.u.). Combined PD/T2 maps are REQUIRED to use this suffix irrespective of the method they are related to. N/A                                                                                                                                                   |
-| RF transmit field map                                  | B1plusmap | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/10-qmri.md) for associated inputs and further details                                                                     |
-| RF receive sensitivity map                                  | B1minusmap | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/10-qmri.md) for associated inputs and further details                                                                     |
+| RF transmit field map                                  | TB1map | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/10-qmri.md) for associated inputs and further details                                                                     |
+| RF receive sensitivity map                                  | RB1map | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/10-qmri.md) for associated inputs and further details                                                                     |
 | Observed signal amplitude map                                | S0map | Parametric   | In arbitrary units (a.u.). For a multi-echo sequence, S0 maps index the baseline signal before exponential (T2*) 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 REQUIRED to use this suffix irrespective of the method they are related to. _Associated suffixes:_ T2starmap.       |
 
 Quantitative maps can be obtained right off the scanner or by processing files
@@ -870,4 +870,4 @@ encoding directions) of the corresponding sequence. Please rely only on the JSON
 file to obtain scanning parameters. \_epi files can be a 3D or 4D - in the
 latter case all timepoints share the same scanning parameters. To indicate which
 run is intended to be used with which functional or diffusion scan the
-IntendedFor field in the JSON file should be used.
\ No newline at end of file
+IntendedFor field in the JSON file should be used.
diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index e0b7f61a73..a35b237733 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -196,7 +196,7 @@ sub-01_T1map.json
            "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_B1plusmap.nii.gz"],
+           "fmap/sub-01_TB1map.nii.gz"],
 
 <<Parameters that are constant across members of VFA grouping suffix>>
 
@@ -243,12 +243,12 @@ maps are stored in the `fmap` folder.
 
 | Name                                       | Suffix  | Type     | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
 |--------------------------------------------|---------|----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| Double-angle B1<sup>+</sup> mapping                    | TB1DAM   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Insko and Bolinger 1993](https://www.sciencedirect.com/science/article/abs/pii/S1064185883711332)). Double angle method 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. _Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
-| B1<sup>+</sup> mapping with 3D EPI            | TB1EPI   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)). This method 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. _Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
-| Actual Flip Ange Imaging (AFI)             | TB1AFI   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Yarnykh 2007](https://dx.doi.org/10.1002/mrm.21120)). This method calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence. _Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
-| Siemens `tfl_b1_map`             | TB1TFL   | RF Grouping | Groups images 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._Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
-| Siemens `rf_map`             | TB1RFM   | RF Grouping | Groups images acquired using `rf_map` product sequence by Siemens, using a method combining SE and STE images with EPI readout similar to that by ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)). The sequence generates one ~anatomical image and one scaled flip angle map. _Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
-| B1<sup>-</sup> field correction          | RB1COR   | RF Grouping | Groups 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). _Associated output suffixes_: `B1minusmap`                                                                                                                                                      |
+| Double-angle B1<sup>+</sup> mapping                    | TB1DAM   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Insko and Bolinger 1993](https://www.sciencedirect.com/science/article/abs/pii/S1064185883711332)). Double angle method 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. _Associated output suffixes_: `TB1map`                                                                                                                                                      |
+| B1<sup>+</sup> mapping with 3D EPI            | TB1EPI   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)). This method 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. _Associated output suffixes_: `TB1map`                                                                                                                                                      |
+| Actual Flip Ange Imaging (AFI)             | TB1AFI   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Yarnykh 2007](https://dx.doi.org/10.1002/mrm.21120)). This method calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence. _Associated output suffixes_: `TB1map`                                                                                                                                                      |
+| Siemens `tfl_b1_map`             | TB1TFL   | RF Grouping | Groups images 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._Associated output suffixes_: `TB1map`                                                                                                                                                      |
+| Siemens `rf_map`             | TB1RFM   | RF Grouping | Groups images acquired using `rf_map` product sequence by Siemens, using a method combining SE and STE images with EPI readout similar to that by ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)). The sequence generates one ~anatomical image and one scaled flip angle map. _Associated output suffixes_: `TB1map`                                                                                                                                                      |
+| B1<sup>-</sup> field correction          | RB1COR   | RF Grouping | Groups 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). _Associated output suffixes_: `RB1map`                                                                                                                                                      |
 
 ## Entity specifications for RF field mapping grouping suffixes
 
@@ -392,10 +392,10 @@ BIDS-apps. For example:
  |   └── qMRI-software/
  |       └── sub-01/
  |           └── fmap/
- |               ├── sub-01_acq-PDw_B1minusmap.nii.gz    ─────────┐ 
- |               ├── sub-01_acq-PDw_B1minusmap.json      ───────┐ | 
- |               ├── sub-01_B1plusmap.nii.gz             ─────┐ | | 
- |               └── sub-01_B1plusmap.json               ───┐ | | | 
+ |               ├── sub-01_acq-PDw_RB1map.nii.gz    ─────────┐ 
+ |               ├── sub-01_acq-PDw_RB1map.json      ───────┐ | 
+ |               ├── sub-01_TB1map.nii.gz             ─────┐ | | 
+ |               └── sub-01_TB1map.json               ───┐ | | | 
  └── sub-01/                                                | | | | S
      └── fmap/                                              | | | | Y
          ├── sub-01_acq-bodyPDw_RB1COR.nii.gz               | | | | M
@@ -406,8 +406,8 @@ BIDS-apps. For example:
          ├── sub-01_fa-1_TB1DAM.json                        | | | | 
          ├── sub-01_fa-2_TB1DAM.nii.gz                      | | | | T
          ├── sub-01_fa-2_TB1DAM.json                        | | | | O
-         ├── sub-01_acq-PDw_B1minusmap.nii.gz  ◀────────────├─├─├─┘
-         ├── sub-01_acq-PDw_B1minusmap.json    ◀────────────├─├─┘
-         ├── sub-01_B1plusmap.nii.gz           ◀────────────├─┘
-         └── sub-01_B1plusmap.json             ◀────────────┘
-```
\ No newline at end of file
+         ├── sub-01_acq-PDw_RB1map.nii.gz  ◀────────────├─├─├─┘
+         ├── sub-01_acq-PDw_RB1map.json    ◀────────────├─├─┘
+         ├── sub-01_TB1map.nii.gz           ◀────────────├─┘
+         └── sub-01_TB1map.json             ◀────────────┘
+```

From 9a0d04b6d265bc103ff5aa4ce1ae66774f266657 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Sat, 13 Jun 2020 08:06:25 -0400
Subject: [PATCH 59/76] Update 10-qmri.md

---
 src/99-appendices/10-qmri.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index 9191b31db8..24e2f1e367 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -37,7 +37,7 @@ 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 varying additional scan parameters.
 
-If such a inheritance relationship is applicable between an already existing
+If such an inheritance relationship is applicable between an already existing
 `grouping suffix` and a new qMRI application to be included in the specification,
 the inheritor qMRI method MUST be listed in the table below instead of
 introducing a new `grouping suffix`. This approach:
@@ -439,4 +439,4 @@ BIDS-apps. For example:
          ├── sub-01_acq-PDw_B1minusmap.json    ◀────────────├─├─┘
          ├── sub-01_B1plusmap.nii.gz           ◀────────────├─┘
          └── sub-01_B1plusmap.json             ◀────────────┘
-```
\ No newline at end of file
+```

From 9834df745f8693739b33c4433c915e35ba740204 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sat, 13 Jun 2020 09:43:37 -0400
Subject: [PATCH 60/76] [UPDATE] qMRI map generation options

---
 src/99-appendices/10-qmri.md | 35 ++++++++++++++++++++++-------------
 1 file changed, 22 insertions(+), 13 deletions(-)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index e703952e1d..e7758ac591 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -127,22 +127,26 @@ All qMRI maps are generated following a set of calculations. Unlike conventional
 MR images, they are not products of an MRI image reconstruction (from k-space data 
 to structural images). There are two possible options in the way a qMRI map is obtained: 
 
-1. The qMRI map is calculated at the scanner site through a non-transparent vendor pipeline.
-2. The qMRI map is generated off-site using open-source software. 
+1. Pre-generated qMRI maps: The qMRI maps are generated immediately after the 
+reconstruction of the multi-contrast 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 on the scanner site.
+2. Post-generated qMRI maps: The qMRI maps are generated from the multi-contrast
+input images after they are exported outside the scanner site.
 
 ## Where to place qMRI maps? 
 
-**If the qMRI map is calculated at the scanner site through a non-transparent vendor pipeline:** 
+**If the provenance record of the qMRI map generation is NOT accessible:**
 
-Although qMRI maps are derivatives, we cannot relate them to their parent images (which may
-not even be accessible) through a set of calculations in this case. Therefore, such maps obtained
-at the scanner site via non-transparent pipelines are placed at the `/sub-#/anat` directory.
+Although qMRI maps are derivatives by definition, we cannot relate them to their 
+multi-contrast input images in this case. Therefore, qMRI maps lacking provenance
+are directly placed at the `/sub-#/anat` directory.
 
-**If the qMRI map is generated using open-source software:**
+**If the provenance record of the qMRI map generation is available:**
 
-Quantitative maps SHOULD be stored in the `derivatives` folder, but MAY
+In this case, qMRI maps SHOULD be stored in the `derivatives` folder, but MAY
 be symbolic linked to the corresponding raw data directory to facilitate the
-easy use of these images as input to processing workflows implemented as
+easy use of these images as inputs to the processing workflows implemented as
 BIDS-apps. For example:
 
 ```diff
@@ -177,11 +181,12 @@ application can easily pick up a qMRI map along with other anatomical images.
 
 ## <a name="whichmetadata">Which metadata fields should a qMRI map contain?</a>
 
-**If the qMRI map is calculated at the scanner site through a non-transparent vendor pipeline:** 
+**If the provenance record of the qMRI map generation is NOT accessible:**
 
-JSON content is confined to the metadata made available by the vendor pipeline.
+JSON content is confined to the metadata made available for the pre-generated
+qMRI map.
 
-**If the qMRI map is generated using open-source software:**
+**If the provenance record of the qMRI map generation is available:**
 
 JSON file of the qMRI map MUST inherit metadata from its parent images (typically a grouped scan 
 collection) by adhering to the following rules:
@@ -408,7 +413,11 @@ entries:
 
 ## Where to place RF field maps? 
 
-**If the RF field map is generated using open-source software:**
+**If the provenance record of the RF field map generation is NOT accessible:**
+
+RF field maps lacking provenance are directly placed at the `/sub-#/fmap` directory.
+
+**If the provenance record of the RF rield map generation is available:**
 
 RF field maps SHOULD be stored in the `derivatives` folder, but MAY
 be symbolic linked to the corresponding raw data directory to facilitate the

From e03a6f525c506c42cba08af3d35a5311d0c2a6a3 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sat, 13 Jun 2020 10:07:44 -0400
Subject: [PATCH 61/76] Add PDT2

---
 .../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 98fae87f0f..786af2ddd2 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
@@ -215,7 +215,8 @@ A change to the specification is REQUIRED to expand or to modify the following t
 | T2 star weighted images                    | T2starw | Conventional | Denotes images with predominant T2* contribution, typically images acquired using a GRE sequence with low flip angle, long echo time and long repetition time. Please note that this suffix is not a surrogate for `T2starmap`. |
 | Fluid Attenuated Inversion Recovery Images | FLAIR   | Conventional | Denotes 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 | Conventional | T1-weighted anatomical image matched to functional acquisition                                                           |
-| Inplane T2                                 | inplaneT2 | Conventional | T2-weighted anatomical image matched to functional acquisition                                                           | 
+| Inplane T2                                 | inplaneT2 | Conventional | T2-weighted anatomical image matched to functional acquisition                                                           |
+| PDw and T2w images obtained using dual-echo FSE           | PDT2| Conventional | PDw and T2w images acquired using a dual-echo FSE sequence through view sharing process [(Johnson et al. 1994)](http://www.ajnr.org/content/15/4/667.short).                                                           | 
 
 Example use for conventional **T1 weighted images**:
 

From e17c8df413e17c5d9e23b759701ad5b52aeced9d Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 14 Jun 2020 08:16:36 -0400
Subject: [PATCH 62/76] [CHANGE] SA2RAGE to TB1SRGE

---
 src/99-appendices/10-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index 0f5c1ad3f5..96a31feb76 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -248,7 +248,7 @@ maps are stored in the `fmap` folder.
 | Actual Flip Ange Imaging (AFI)             | TB1AFI   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Yarnykh 2007](https://dx.doi.org/10.1002/mrm.21120)). This method calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence. _Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
 | Siemens `tfl_b1_map`             | TB1TFL   | RF Grouping | Groups images 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._Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
 | Siemens `rf_map`             | TB1RFM   | RF Grouping | Groups images acquired using `rf_map` product sequence by Siemens, using a method combining SE and STE images with EPI readout similar to that by ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)). The sequence generates one ~anatomical image and one scaled flip angle map. _Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
-|Saturation‐prepared with 2 rapid Gradient Echoes (SA2RAGE) B1<sup>+</sup> mapping | SA2RAGE | RF Grouping |Groups images for  B1+ field mapping ([Eggenschwiler et al. 2011](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.23145)). SA2RAGE uses a ratio of two saturation recovery images with different time delays, and a simulated look-up table to estimate B1+. This sequence can also be used in conjunction with MP2RAGE T1 mapping to iteratively improve B1+ and T1 map estimation ([Marques & Gruetter 2013](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069294)). Associated output suffixes: B1plusmap                                                                                                                                                     |
+|Saturation‐prepared with 2 rapid Gradient Echoes (SA2RAGE) B1<sup>+</sup> mapping | TB1SRGE | RF Grouping |Groups images for  B1+ field mapping ([Eggenschwiler et al. 2011](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.23145)). SA2RAGE uses a ratio of two saturation recovery images with different time delays, and a simulated look-up table to estimate B1+. This sequence can also be used in conjunction with MP2RAGE T1 mapping to iteratively improve B1+ and T1 map estimation ([Marques & Gruetter 2013](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069294)). Associated output suffixes: B1plusmap                                                                                                                                                     |
 | B1<sup>-</sup> field correction          | RB1COR   | RF Grouping | Groups 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). _Associated output suffixes_: `B1minusmap`                                                                                                                                                      |
 
 ## Entity specifications for RF field mapping grouping suffixes

From 7950b84e3c4d7b8ac3e64c764f6058d7dc91b3ca Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 14 Jun 2020 08:27:08 -0400
Subject: [PATCH 63/76] [ADD] Cahnges by @ChristophePhillips

---
 src/99-appendices/10-qmri.md | 41 +++++++++++++++++++++++-------------
 1 file changed, 26 insertions(+), 15 deletions(-)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index 040f417025..30ee16f349 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -272,13 +272,13 @@ maps are stored in the `fmap` folder.
 
 | Name                                       | Suffix  | Type     | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
 |--------------------------------------------|---------|----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| Double-angle B1<sup>+</sup> mapping                    | TB1DAM   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Insko and Bolinger 1993](https://www.sciencedirect.com/science/article/abs/pii/S1064185883711332)). Double angle method 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. _Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
-| B1<sup>+</sup> mapping with 3D EPI            | TB1EPI   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)). This method 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. _Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
-| Actual Flip Ange Imaging (AFI)             | TB1AFI   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Yarnykh 2007](https://dx.doi.org/10.1002/mrm.21120)). This method calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence. _Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
-| Siemens `tfl_b1_map`             | TB1TFL   | RF Grouping | Groups images 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._Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
-| Siemens `rf_map`             | TB1RFM   | RF Grouping | Groups images acquired using `rf_map` product sequence by Siemens, using a method combining SE and STE images with EPI readout similar to that by ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)). The sequence generates one ~anatomical image and one scaled flip angle map. _Associated output suffixes_: `B1plusmap`                                                                                                                                                      |
-|Saturation‐prepared with 2 rapid Gradient Echoes (SA2RAGE) B1<sup>+</sup> mapping | TB1SRGE | RF Grouping |Groups images for  B1+ field mapping ([Eggenschwiler et al. 2011](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.23145)). SA2RAGE uses a ratio of two saturation recovery images with different time delays, and a simulated look-up table to estimate B1+. This sequence can also be used in conjunction with MP2RAGE T1 mapping to iteratively improve B1+ and T1 map estimation ([Marques & Gruetter 2013](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069294)). Associated output suffixes: B1plusmap                                                                                                                                                     |
-| B1<sup>-</sup> field correction          | RB1COR   | RF Grouping | Groups 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). _Associated output suffixes_: `B1minusmap`                                                                                                                                                      |
+| Double-angle B1<sup>+</sup> mapping                    | TB1DAM   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Insko and Bolinger 1993](https://www.sciencedirect.com/science/article/abs/pii/S1064185883711332)). Double angle method 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. _Associated output suffixes_: `TB1map`                                                                                                                                                      |
+| B1<sup>+</sup> mapping with 3D EPI            | TB1EPI   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)). This method 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. _Associated output suffixes_: `TB1map`                                                                                                                                                      |
+| Actual Flip Ange Imaging (AFI)             | TB1AFI   | RF Grouping | Groups images for B1<sup>+</sup> field mapping ([Yarnykh 2007](https://dx.doi.org/10.1002/mrm.21120)). This method calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence. _Associated output suffixes_: `TB1map`                                                                                                                                                      |
+| Siemens `tfl_b1_map`             | TB1TFL   | RF Grouping | Groups images 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._Associated output suffixes_: `TB1map`                                                                                                                                                      |
+| Siemens `rf_map`             | TB1RFM   | RF Grouping | Groups images acquired using `rf_map` product sequence by Siemens, using a method combining SE and STE images with EPI readout similar to that by ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)). The sequence generates one ~anatomical image and one scaled flip angle map. _Associated output suffixes_: `TB1map`                                                                                                                                                      |
+|Saturation‐prepared with 2 rapid Gradient Echoes (SA2RAGE) B1<sup>+</sup> mapping | TB1SRGE | RF Grouping |Groups images for  B1+ field mapping ([Eggenschwiler et al. 2011](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.23145)). SA2RAGE uses a ratio of two saturation recovery images with different time delays, and a simulated look-up table to estimate B1+. This sequence can also be used in conjunction with MP2RAGE T1 mapping to iteratively improve B1+ and T1 map estimation ([Marques & Gruetter 2013](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069294)). Associated output suffixes: TB1map                                                                                                                                                     |
+| B1<sup>-</sup> field correction          | RB1COR   | RF Grouping | Groups 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). _Associated output suffixes_: `RB1map`                                                                                                                                                      |
 
 
 ## Entity specifications for RF field mapping grouping suffixes
@@ -302,19 +302,30 @@ The `fa` and `echo` entities MUST be used to distinguish images with this suffix
 The use of `fa` follows the default convention. However, this suffix defines a
 specific use case for the `echo` entity:
 
-At each `FlipAngle`, the `TB1EPI` suffix lists two images acquired at two echo times.
-However, the second echo in this method is generated in a different fashion compared 
-to the `MESE`. The first echo is a typical spin echo (SE), whereas the second
-echo is a stimulated echo (STE) that is not generated by an inversion pulse. 
-
-To properly identify constituents of this particular method, values of the `echo`
-entity MUST index the images as follows:  
-
 |`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/

From 6f1ed2fa2f1bdcf8b2c89f9aeb99972530d162e3 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Sun, 14 Jun 2020 16:20:10 -0400
Subject: [PATCH 64/76] Update definition

---
 .../01-magnetic-resonance-imaging-data.md     | 32 ++++++++++++++-----
 1 file changed, 24 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 c4c40cea31..8a023ecaad 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
@@ -113,8 +113,8 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     anat/
-        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_ce-<label>][_rec-<label>][_run-<index>]_<suffix>.nii[.gz]
-        sub-<label>[_ses-<label>][_acq-<label>][_part-<mag/phase>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<suffix>]_defacemask.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_part-<label>][_ce-<label>][_rec-<label>][_run-<index>]_<suffix>.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_part-<label>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<suffix>]_defacemask.nii[.gz]
 ```
 
 The term anatomical imaging data pertains to a broad range of MRI applications that provide structural 
@@ -317,13 +317,29 @@ description of the `T1map` suffix requires the parameter to be in seconds (s).
 
 #### The `part` entity
 
-Some applications depends on `magnitude` and `phase` reconstructed images for the 
-calculation of a parameter map. In such case two files could have the following 
-names: `sub-01_part-mag_T1w.nii.gz` and `sub-01_part-phase_T1w.nii.gz`. 
+This entity shall be 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](https://dicom.innolitics.com/ciods/enhanced-mr-image/enhanced-mr-image/00089208). Allowed label values for this entity are 
+`phase`, `mag`, `real` and `imag`, which are typically used in `mag/phase` or 
+`real/imag` pairs. For example:
 
-Phase images SHOULD be in radians and have a range of (0, 2 pi] (including 0, 
-excluding 2 pi). The `part-<mag/phase>` key/value pair is associated with the 
-DICOM tag [0008,9208](https://dicom.innolitics.com/ciods/enhanced-mr-image/enhanced-mr-image/00089208).
+```
+sub-01_part-mag_T1w.nii.gz 
+sub-01_part-mag_T1w.json
+sub-01_part-phase_T1w.nii.gz 
+sub-01_part-phase_T1w.json
+```
+
+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:  `radians` or 
+`a.u.` for grayscale images. For example: 
+
+sub-01_part-phase.json
+```
+{
+   "Units": "radians"
+}
+```
 
 #### The `run` entity
 

From 469c0cf746753806d7aaa374679280bad841be8f Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Wed, 17 Jun 2020 12:14:55 +0200
Subject: [PATCH 65/76] Some textual changes

---
 src/99-appendices/10-qmri.md | 64 +++++++++++++++++++++---------------
 1 file changed, 38 insertions(+), 26 deletions(-)

diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/10-qmri.md
index 60fc92355f..6880805e67 100644
--- a/src/99-appendices/10-qmri.md
+++ b/src/99-appendices/10-qmri.md
@@ -1,9 +1,10 @@
+This appendix contains detailed information on how to organize quantitative MRI
+data in the BIDS format.
+
 # Method-specific priority levels for grouping suffix
 
-Although there is not an upper limit to the amount of metadata
-for images collected by a `grouping suffix`, some of the metadata entries become
-REQUIRED when considered within the context of a specific qMRI
-application.
+Some of the metadata entries are REQUIRED for specific qMRI methods.
+These metadata are laid-out in the table below.
 
 <a name="prioritylevels">Table of method-specific priority levels for qMRI metadata</a>
 
@@ -25,11 +26,15 @@ Explanation of the table:
 minimum viable qMRI application for the corresponding `grouping suffix`.
 * Note that some of the metadata fields may be unaltered across different members
 of a given `grouped scan collection`, yet still needed as an input to a qMRI
-model for parameter fitting (e.g. `RepetitionTimeExcitation` of `VFA`). 
+model for parameter fitting (e.g. `RepetitionTimeExcitation` of `VFA`) and therefore
+should be included in all json-sidecars. 
 * The metadata fields listed in the OPTIONAL column can be used to derive
-various qMRI applications from an existing `grouping suffix`. The following section expands on the set of rules to derive qMRI applications from an existing `grouping suffix`.
+various qMRI applications from an existing `grouping suffix`. 
+
+The following section expands on the set of rules to derive novel qMRI applications
+from an existing `grouping suffix`.
 
-# qMRI applications that can be derived from an existing `grouping suffix`
+# How to derive the intended qMRI application from an ambiguous `grouping suffix`
 
 Certain grouping suffixes may refer to a generic data collection regime such as
 variable flip angle (VFA), rather than a more specific acquisition, e.g.,
@@ -62,10 +67,11 @@ specification.
  constituent images of the respective `grouping suffix`, fixed otherwise (`fix`). 
  If the OPTIONAL metadata type is `var`, respective naming entities can be found in the 
  OPTIONAL entities column of [`grouping suffix` table](#grouping-suffix). 
-*** 
+
+* * *
 
 A derived qMRI application becomes avaiable if all the OPTIONAL metadata fields
-listed for a `grouping suffix` is provided in the data. In addition, conditional
+listed for a `grouping 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 `grouping suffix`. 
@@ -79,7 +85,10 @@ T2 fitting application. Finally, if the `DESPOT2` data has more than one
 `SpoilingRFPhaseIncrement` field as a metadata field, then the dataset is valid
 for `DESPOT2-FM`. In this case, `rfphase` entity can be used to distinguish inputs. 
 
-Please note that OPTIONAL metadata fields listed in the [qMRI applications that can be derived from an existing suffix table](#varianttable) MUST be also included in the [method sprecific priority levels for qMRI metadata table](#prioritylevels)  for the sake of completeness.
+Please note that OPTIONAL metadata fields listed in the 
+qMRI applications that can be derived from an existing suffix table](#varianttable) MUST
+also be included in the
+[method sprecific priority levels for qMRI metadata table](#prioritylevels) for the sake of completeness.
 
 Please also note that the rules concerning the presence/value of certain metadata
 fields within the context of `grouping suffix` is not a part of the BIDS
@@ -110,15 +119,16 @@ application (e.g. `MP2RAGE`), sequence names are NOT used as grouping suffixes.
 grouping suffix by defining a set of logical conditions over the metadata
 fields, the [table of method-specific priority levels](#prioritylevels) and the
 [table of qMRI applications that can be derived from an existing grouping suffix](#varianttable)
- MUST be expanded instead of introducing a new grouping suffix.
- Please visit the [JSON content for grouping suffixes](#whichmetadata) 
- for further details.
+MUST be expanded instead of introducing a new grouping suffix.
+Please visit the [JSON content for grouping suffixes](#whichmetadata) 
+for further details.
 * Please note that if a structural data has the type of grouped scan collection,
 the use of `_suffix` alone cannot distinguish its members from each other,
 failing to identify their roles as inputs to the calculation of qMRI maps.
 Although such images are REQUIRED to be grouped by a proper grouping suffix,
 they are also RECOMMENDED to include at least one of the `acq`, `part`, `echo`,
-`met`, `inv`-key/value-pairs (please visit corresponding sections for details).
+`met`, `inv`-key/value-pairs  to indicate which scanning parameters are 
+systematically altered.
 
 
 # Management of the qMRI maps
@@ -130,9 +140,9 @@ to structural images). There are two possible options in the way a qMRI map is o
 1. Pre-generated qMRI maps: The qMRI maps are generated immediately after the 
 reconstruction of the multi-contrast 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 on the scanner site.
+or (b) open-source pipelines deployed at the scanner site.
 2. Post-generated qMRI maps: The qMRI maps are generated from the multi-contrast
-input images after they are exported outside the scanner site.
+input images after they are exported outside of the scanner site.
 
 ## Where to place qMRI maps? 
 
@@ -205,7 +215,7 @@ in the following table for the sake of provenance.
 
 | Field name                  | Definition                                                     |
 | :-------------------------- | :------------------------------------------------------------- |
-| BasedOn | List of files grouped by an `grouping suffix` to generate the map. The fieldmaps are also listed, if involved in the processing. |
+| BasedOn | List of files grouped by an `grouping suffix` 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.)|
 | EstimationSoftwareName | The name of the open-source tool used for fitting (e.g. [qMRLab](https://qmrlab.org), [QUIT](https://github.com/spinicist/QUIT), [hMRI-Toolbox](https://hmri-group.github.io/hMRI-toolbox/) etc.)|
@@ -263,15 +273,17 @@ sub-01_T1map.json
 
 # Radiofrequency (RF) field mapping 
 
-Most qMRI methods are susceptible to the nonuniformities in the transmit (B1<sup>+</sup>) and/or receive (B1<sup>-</sup>) radiofrequency (RF) fields. Various (acquisition based)
-methods are available to derive maps of spatial variations in the B1<sup>+</sup> and B1<sup>-</sup> 
-fields. These maps are commonly used for the correction of qMRI estimation errors 
-arising from the imperfections in the respective RF field.
-
-An approach similar to that used in anatomical MR images to group a set of input images intended
-for qMRI application (`grouping suffix`) is applied for the inputs of B1<sup>+</sup> and B1<sup>-</sup> RF field mapping. Note that these images do not convey substantial
-structural information by design. Therefore, both inputs and outputs of RF field
-maps are stored in the `fmap` folder.
+Most qMRI methods are susceptible to nonuniformities in the transmit (B1<sup>+</sup>)
+and/or receive (B1<sup>-</sup>) radiofrequency (RF) fields. Various (acquisition based)
+methods are available to derive maps of spatial variations in the B1<sup>+</sup>
+and B1<sup>-</sup> fields. These maps are commonly used for the correction of qMRI
+estimation errors arising from the imperfections in the respective RF field.
+
+An approach similar to that used in anatomical MR images to group a set of input images
+intended for qMRI application (`grouping suffix`) is applied for the inputs of
+B1<sup>+</sup> and B1<sup>-</sup> RF field mapping. Note that these images do not
+convey substantial structural information by design. Therefore, both inputs and
+outputs of RF field maps are stored in the `fmap` folder.
 
 ## Grouping suffixes for RF field mapping 
 

From 0e163981f22b60dd0604c264965854305b79b412 Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Wed, 17 Jun 2020 16:12:51 +0200
Subject: [PATCH 66/76] Added BEP-001 contributors

---
 src/99-appendices/01-contributors.md | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/src/99-appendices/01-contributors.md b/src/99-appendices/01-contributors.md
index a5b76298dc..ad6eec4a22 100644
--- a/src/99-appendices/01-contributors.md
+++ b/src/99-appendices/01-contributors.md
@@ -41,8 +41,10 @@ your name is not listed, please add it.
 -   Eric Bridgeford 📖🔧
 -   Teon L. Brooks 📖💻⚠️💬👀🤔🔧🐛📢
 -   Suyash Bhogawar 📖💡⚠️🔧💬
+-   Mathieu Boudreau 📖
 -   Vince D. Calhoun 📖
 -   Alexander L. Cohen 🐛💻📖💬
+-   Julien Cohen-Adad 📖
 -   R. Cameron Craddock 📖📢
 -   Sasha D'Ambrosio 📖
 -   Samir Das 📖
@@ -81,14 +83,17 @@ your name is not listed, please add it.
 -   Dora Hermes 📖💻✅🔍🤔
 -   Katja Heuer 🔧
 -   Chris Holdgraf 📖🤔
+-   Gilles de Hollander 📖🤔💡
 -   Christopher J. Honey 📖
 -   Jean-Christophe Houde 📖
 -   International Neuroinformatics Coordinating Facility 💵📋
 -   Andrew Janke 📖💻
 -   Mainak Jas 📖💻
 -   Alexander Jones 💻🐛
+-   Agâh Karakuzu 📖🤔💡
 -   David Keator 📖
 -   James Kent 💬💻
+-   Ali Khan 📖🤔
 -   Gregory Kiar 📖💻🎨🔧
 -   Robert Knight 📖
 -   Jean-Philippe Lachaux 📖
@@ -98,17 +103,21 @@ your name is not listed, please add it.
 -   Laura and John Arnold Foundation 💵
 -   Christopher Lee-Messer 📖
 -   Jon Haitz Legarreta 💻📖
+-   Ilana Leppert 📖
+-   Tobias Leutritz 📖
 -   Xiangrui Li 📖💻
 -   Vladimir Litvak 📖
 -   Brian N. Lundstrom 📖
 -   Dan Lurie 🤔📖🔧🔌💻💬
 -   Camille Maumet 📖
 -   Christopher J. Markiewicz 💬🐛💻📖🎨💡🤔🔌👀🔧📢
+-   José Marques 🤔
 -   Kai J. Miller 📖
 -   Jeremy Moreau 📖💡
 -   Zachary Michael 📖
 -   Ezequiel Mikulan 📖💻
 -   Michael P. Milham 💡🔍
+-   Martijn Mulder 📖🤔
 -   Henk Mutsaerts 📖
 -   National Institute of Mental Health 💵
 -   Mikael Naveau 🐛
@@ -143,8 +152,10 @@ your name is not listed, please add it.
 -   Matt Sanderson 📖💻
 -   Gunnar Schaefer 📖
 -   Jan-Mathijs Schoffelen 📖
+-   Julien Sein 📖
 -   Robert E. Smith 💻📖
 -   Vanessa Sochat 📖
+-   Isla Staden 📖
 -   Arjen Stolk 📖
 -   Nicole C. Swann 📖
 -   François Tadel 📖🔌💡
@@ -157,6 +168,8 @@ your name is not listed, please add it.
 -   Joseph Wexler 📖💡
 -   Kirstie Whitaker 📖💡🔍🤔📢💬
 -   Jonathan Winawer 📖
+-   Tobias Wood 📖
 -   Gaël Varoquaux 📖
 -   Tal Yarkoni 💻📖🤔🔍🔌👀📢🐛🎨
 -   Lyuba Zehl 📖
+-   Wietske van der Zwaag 📖🤔💡

From 3fbfdb720426aeb999903e89e208cb7319312c8a Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Wed, 17 Jun 2020 16:50:24 +0200
Subject: [PATCH 67/76] Some minor textual changes

---
 .../01-magnetic-resonance-imaging-data.md     | 106 ++++++++++++------
 1 file changed, 70 insertions(+), 36 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 0e7c153004..3026112643 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
@@ -46,7 +46,7 @@ by Ben Inglis:
 | SpoilingState            | RECOMMENDED. Boolean value (`true` or `false`), specifying whether the pulse sequence uses any type of spoiling stratey to suppress transverse magnetization remaining after the readout. |
 | SpoilingType             | RECOMMENDED. Specifies which spoiling method(s) are used by a spoiled sequence. Accepted values: `RF`, `GRADIENT` or `COMBINED`.                                                          |
 | SpoilingRFPhaseIncrement | RECOMMENDED. 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. Zeroth moment of the spoiler gradient lobe in militesla times second per meter (mT.s/m).                                                                                     |
+| SpoilingGradientMoment   | RECOMMENDED. Zeroth moment of the spoiler gradient lobe in millitesla times second per meter (mT.s/m).                                                                                     |
 | SpoilingGradientDuration | RECOMMENDED. 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
@@ -135,7 +135,7 @@ information about (brain) anatomy, but differ by the nature of the data they con
 1. a single image with specific weighting on an arbitrary scale (e.g. a 3D high resolution T1-weighted image).
 This type is most commonly used in neuroimaging applications.
 2. a group of images acquired within a single protocol for the purpose of improving contrast 
-characteristics (e.g., a multi-echo anatomical GRE image) or calculating quantitative maps
+characteristics (e.g., a set of multi-echo anatomical GRE images) or calculating quantitative maps
 (e.g. four 3D volumes provided as an input to an MP2RAGE calculation) 
 3. a quantitative map of which the intensities are put on an absolute scales (e.g., seconds for a T1 map).
 These images are generally produced by some mathematical operation on images from class 2.
@@ -143,16 +143,16 @@ These images are generally produced by some mathematical operation on images fro
 #### Conventional structural acquisitions
 
 Anatomical images of this type typically refer to a volumetric high-resolution 
-dataset, representing the measured MRI signal in an arbitrary scale of gray
-shades. Contrast factor of these grayscale images depend on the relative contribution
+dataset, representing the measured MRI signal in an arbitrary scale of "gray
+shades". Contrast factor of these grayscale images depend on the relative contribution
 of inherent tissue parameters (e.g. `T1`, `T2` and `PD`) to the measured signal. 
 
 Contribution weights of these parameters are determined by the type of acquisition
 sequence (e.g. `spin-` or `gradient-echo`) and the setting of various parameters
 (e.g. `Repetition Time`, `Echo Time`, `Inversion Time` and `Flip Angle`). For 
 example, in a spoiled gradient-echo scan, keeping the repetition and the echo time 
-short with a relatively large flip angle increases the contribution of `T1`, yielding
-a primarily T1-weighted image.
+short with a relatively large flip angle increases the contribution of `T1` effects
+to the image contrast, yielding a primarily T1-weighted image.
 
 #### Grouped scan collections for contrast improvement or quantitative map calculation
 
@@ -160,9 +160,13 @@ A group of anatomical scans may be collected to enhance certain contrast feature
 such as to calculate a weighted average of multi-echo gradient echo (`MEGRE`) images,
 which is known to improve segmentation algorithm outputs.
 
-Quantitative MRI (qMRI) methods mathematically characterize the signal changes observed in a collection of parametrically altered scans under certain biophysical model assumptions. These `grouped scan collections` are then processed to derive a `qMRI map`, representing anatomical features in a physically meaningful parameter range.
+Quantitative MRI (qMRI) methods mathematically characterize the signal changes observed
+in a collection of parametrically altered scans under certain biophysical model assumptions.
+These `grouped scan collections` can then be processed to derive a `qMRI map`, representing
+anatomical features in a physically meaningful parameter range.
 
-In both cases, the contrast characteristics change with varying acquisition parameters across `grouped scan collections`. Therefore, it is not tenable to name all the members
+In both cases, the contrast characteristics change with varying acquisition parameters across
+`grouped scan collections`. Therefore, it is not tenable to name all the members
 of a `grouped scan collection` with one conventional MRI suffix label (e.g., `T1w`)
 or any other label that implies interchangeability among its instances. 
 
@@ -213,7 +217,7 @@ A change to the specification is REQUIRED to expand or to modify the following t
 | T1 weighted images                         | T1w     | Conventional | Denotes images with predominant T1 contribution.                                                                                                                                                                                |
 | T2 weighted images                         | T2w     | Conventional | Denotes images with predominant T2 contribution.                                                                                                                                                                                |
 | Proton density weighted images             | PDw     | Conventional | Denotes images with predominant proton density (PD) contribution.                                                                                                                                                               |
-| T2 star weighted images                    | T2starw | Conventional | Denotes images with predominant T2* contribution, typically images acquired using a GRE sequence with low flip angle, long echo time and long repetition time. Please note that this suffix is not a surrogate for `T2starmap`. |
+| T2 star weighted images                    | T2starw | Conventional | Denotes images with predominant T2\* contribution. Please note that this suffix is not a surrogate for `T2starmap`. |
 | Fluid Attenuated Inversion Recovery Images | FLAIR   | Conventional | Denotes 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 | Conventional | T1-weighted anatomical image matched to functional acquisition                                                           |
 | Inplane T2                                 | inplaneT2 | Conventional | T2-weighted anatomical image matched to functional acquisition                                                           |
@@ -240,8 +244,7 @@ If an anatomical image is defaced for anonymization, one MAY provide
 the binary mask that was used to remove facial features. In the specific case of
 naming this binary mask, the `_<suffix>` entity is replaced by `_<defacemask>` entry.
 Therefore, to contain the original `_<suffix>` entry, the OPTIONAL `mod-<suffix>`
-entity is used. For example, deface mask image belonging to a **T1 weighted image**
-is named as follows:
+entity is used. For example, deface mask image belonging to a **T1 weighted image** is named as follows:
 
 ```
 sub-01_mod-T1w_defacemask.nii.gz
@@ -251,20 +254,27 @@ sub-01_mod-T1w_defacemask.json
 
 **Function:**
 
-Files that belong to a **grouped scan collection** are part of a single scan protocol that acquires multiple images with  similar acquisition parameters and is intended to a) increase contrast by combining multiple similar images (e.g., a multi-echo GRE), or b) to estimate physical parameters on an absolute scale, within a qMRI analysis framework (e.g., a T1-map using a MP2RAGE-protocol).
-The quantitative maps that are output from these calculations (e.g., `T1map`, `T2map` etc) are described in the [qMRI map suffixes](#qmri-map-suffixes) section below.
-A change to the specification is REQUIRED to expand or to modify the following table.
+Files that belong to a **grouped scan collection** are part of a single scan
+protocol that acquires multiple images with  similar acquisition parameters
+that are systematically altered. Grouped scan collections are intended to
+a) increase contrast by combining multiple similar images (e.g., a multi-echo
+GRE), or b) to estimate physical parameters on an absolute scale, within a
+qMRI analysis framework (e.g., a T1-map using a MP2RAGE-protocol). The
+quantitative maps that are output from these calculations (e.g., `T1map`,
+`T2map` etc) are described in the [qMRI map suffixes](#qmri-map-suffixes)
+section below.  A change to the specification is REQUIRED to expand or to
+modify the following table.
 
 | Name                                       | Suffix  | Type     | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
 |--------------------------------------------|---------|----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| Variable flip angle                        | VFA     | Grouping | Parametrically linked anatomical images (primarily) for relaxometry mapping. 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)). Please visit the [qMRI appendix](#prioritylevels) for details. _Associated output suffixes_: T1map, T2map, R1map, R2map |
-| Inversion recovery (for T1 mapping)        | IRT1    | Grouping | Parametrically linked anatomical images for 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)). _Associated output suffixes_: T1map, R1map                                                                                                                                                                                                                                                                                                                    |
-| Magnetization prepared two gradient echoes | MP2RAGE | Grouping | Parametrically linked anatomical images (primarily) for T1 mapping. 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)). _Associated output suffixes_: T1map, R1map, UNIT1                                                                                                                                                                                                                 |
-| Multi-echo spin echo                       | MESE    | Grouping | Parametrically linked anatomical images (primarily) for T2 mapping.The MESE method involves multiple spin echo images acquired at different echo times. _Associated output suffixes_: T2map, R2map, MWFmap                                                                                                                                                                                                                                                                                                                         |
-| Multi-echo gradient echo                   | MEGRE   | Grouping | Parametrically linked multiple anatomical gradient echo images acquired at different echo times. _Associated output suffixes_: T2starmap, R2starmap                                                                                                                                                                                                                                                                                                                                             |
-| Magnetization transfer ratio               | MTR     | Grouping | Parametrically linked anatomical images for calculating a semi-quantitative magnetization transfer ratio map. _Associated output suffixes_: MTRmap                                                                                                                                                                                                                                                                                                                                                                                 |
-| Magnetization transfer saturation          | MTS     | Grouping | Parametrically linked anatomical images for calculating 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)). _Associated output suffixes_: T1map, MTsat                                                                                                                                                                                               |
-| Multi-parametric mapping                   | MPM     | Grouping | Parametrically linked anatomical images for multiparametric mapping (a.k.a hMRI). The MPM approaches 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.,_Associated output suffixes_:R1map, R2starmap, MTsat, PDmap, T1map, T2starmap                                               |
+| Variable flip angle                        | VFA     | Grouping | 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)). Please visit the [qMRI appendix](#prioritylevels) for details. _Associated output suffixes_: T1map, T2map, R1map, R2map |
+| Inversion recovery (for T1 mapping)        | IRT1    | Grouping | 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)). _Associated output suffixes_: T1map, R1map                                                                                                                                                                                                                                                                                                                    |
+| Magnetization prepared two gradient echoes | MP2RAGE | Grouping | 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)). _Associated output suffixes_: T1map, R1map, UNIT1                                                                                                                                                                                                                 |
+| Multi-echo spin echo                       | MESE    | Grouping | The MESE method involves multiple spin echo images acquired at different echo times and is primarily used for T2 mapping. _Associated output suffixes_: T2map, R2map, MWFmap                                                                                                                                                                                                                                                                                                                         |
+| Multi-echo gradient echo                   | MEGRE   | Grouping | Anatomical gradient echo images acquired at different echo times. _Associated output suffixes_: T2starmap, R2starmap                                                                                                                                                                                                                                                                                                                                             |
+| Magnetization transfer ratio               | MTR     | Grouping | Anatomical images for calculating a semi-quantitative magnetization transfer ratio map. _Associated output suffixes_: MTRmap                                                                                                                                                                                                                                                                                                                                                                                 |
+| Magnetization transfer saturation          | MTS     | Grouping | Anatomical images for calculating 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)). _Associated output suffixes_: T1map, MTsat                                                                                                                                                                                               |
+| Multi-parametric mapping                   | MPM     | Grouping | Anatomical images for multiparametric mapping (a.k.a hMRI). The MPM approaches 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.,_Associated output suffixes_:R1map, R2starmap, MTsat, PDmap, T1map, T2starmap                                               |
 
 For example:
 
@@ -279,10 +289,13 @@ Please see the [entity table appendix]() for the REQUIRED and OPTIONAL entities
 for each `grouping suffix`. 
 
 Note that every image in a **grouped scan collection** has the same `_<suffix>` 
-as they are likely to be used together.
-Although the acquisitions will have many identical acquisition parameters, only one-to-one-mapping is allowed between a `.json`-sidecar file and an image in a 
-grouped scan collection. This follows directly from the [inheritance principles of BIDS](../02-common-principles.md#the-inheritance-principle): parameter values that are identical 
-across a set of grouped scans will still have to be stored separately in each `.json`-sidecar file.
+as they are supposed to be used together. Although the acquisitions will have
+many identical acquisition parameters, only one-to-one-mapping is allowed
+between a `.json`-sidecar file and an image in a grouped scan collection.
+This follows directly from the
+[inheritance principles of BIDS](../02-common-principles.md#the-inheritance-principle):
+parameter values that are identical across a set of grouped scans will still
+have to be stored separately in each `.json`-sidecar file.
 
 ##### qMRI map suffixes 
 
@@ -298,20 +311,20 @@ expand or to modify the following table.
 |--------------------------------------------------------|-----------|--------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
 | Longitudinal relaxation time map                       | T1map     | Parametric   | In seconds (s). T1 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `VFA`, `IRT1`, `MP2RAGE`, `MTS`,`MPM`. 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     | Parametric   | In seconds (s). T2 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`, `MPM`                                                                                                                                       |
-| Observed transverse relaxation time map                | T2starmap | Parametric   | In seconds (s). T2* maps are REQUIRED to use this suffix irrespective of the method they are related to._Can be generated from:_ `MEGRE`, `MPM`                                                                                                                                      |
+| Observed transverse relaxation time map                | T2starmap | Parametric   | In seconds (s). T2\* maps are REQUIRED to use this suffix irrespective of the method they are related to._Can be generated from:_ `MEGRE`, `MPM`                                                                                                                                      |
 | Longitudinal relaxation rate map                       | R1map     | Parametric   | In seconds-1 (1/s). R1 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `VFA`, `IRT1`, `MP2RAGE`, `MTS`, `MPM`                                                                                                           |
 | True transverse relaxation rate map                    | R2map     | Parametric   | In seconds-1 (1/s). R2 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`, `MPM`                                                                                                                                  |
-| Observed transverse relaxation rate map                | R2starmap | Parametric   | In seconds-1 (1/s). R2* maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_`MEGRE`, `MPM`                                                                                                                                 |
+| Observed transverse relaxation rate map                | R2starmap | Parametric   | In seconds-1 (1/s). R2\* maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_`MEGRE`, `MPM`                                                                                                                                 |
 | Proton density map                                     | PDmap     | Parametric   | In arbitrary units (a.u.). PD maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MPM`                                                                                                                                    |
 | Magnetization transfer ratio map                       | MTRmap    | Parametric   | In percentage (%). MTR maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MTR`                                                                                                                                           |
 | Magnetization transfer saturation index map            | MTsat     | Parametric   | In arbitrary units (a.u.). MTsat maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MTS`, `MPM`                                                                                                                          |
-| Homogeneous (flat) T1-weighted image by MP2RAGE                 | UNIT1     | Parametric   | 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. _Can be generated from:_ `MP2RAGE`                                                                                                                             |
+| Homogeneous (flat) T1-weighted image by MP2RAGE                 | UNIT1     | Parametric   | 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` _Can be generated from:_ `MP2RAGE`                                                                                                                             |
 | Longutidunal relaxation in rotating frame (T1 rho) map | T1rho     | Parametric   | In seconds (s). T1-rho maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ N/A                                                                                                                                             |
 | Myelin water fraction map                              | MWFmap    | Parametric   | In percentage (%). MWF maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`                                                                                                                                          |
 | Combined PD/T2 map                                     | PDT2map   | Parametric   | In arbitrary units (a.u.). Combined PD/T2 maps are REQUIRED to use this suffix irrespective of the method they are related to. N/A                                                                                                                                                   |
 | RF transmit field map                                  | TB1map | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/10-qmri.md) for associated inputs and further details                                                                     |
 | RF receive sensitivity map                                  | RB1map | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/10-qmri.md) for associated inputs and further details                                                                     |
-| Observed signal amplitude map                                | S0map | Parametric   | In arbitrary units (a.u.). For a multi-echo sequence, S0 maps index the baseline signal before exponential (T2*) 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 REQUIRED to use this suffix irrespective of the method they are related to. _Associated suffixes:_ T2starmap.       |
+| Observed signal amplitude map                                | S0map | Parametric   | In arbitrary units (a.u.). For a multi-echo sequence, S0 maps index the baseline signal before exponential (T2\*) 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 REQUIRED to use this suffix irrespective of the method they are related to. _Associated suffixes:_ T2starmap.       |
 | Quantitative susceptibility map (QSM)                   | Chimap | Parametric   | In parts per million (ppm). QSM allows for determining the underlying magnetic susceptibility of tissue (Chi).  Chi-maps are usually constructed from the phase images of GRE sequences. Chi-maps are quantitative and are reconstructed by solving the magnetic field to susceptibility source inverse problem ([Wang & Liu, 2014](https://onlinelibrary.wiley.com/doi/10.1002/mrm.25358)). |
 
 Quantitative maps can be obtained right off the scanner or by processing files
@@ -334,9 +347,10 @@ description of the `T1map` suffix requires the parameter to be in seconds (s).
 
 This entity shall be 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](https://dicom.innolitics.com/ciods/enhanced-mr-image/enhanced-mr-image/00089208). Allowed label values for this entity are 
-`phase`, `mag`, `real` and `imag`, which are typically used in `mag/phase` or 
-`real/imag` pairs. For example:
+associated with the DICOM tag
+[0008,9208](https://dicom.innolitics.com/ciods/enhanced-mr-image/enhanced-mr-image/00089208).
+Allowed label values for this entity are `phase`, `mag`, `real` and `imag`,
+which are typically used in `mag/phase` or `real/imag` pairs. For example:
 
 ```
 sub-01_part-mag_T1w.nii.gz 
@@ -356,6 +370,9 @@ sub-01_part-phase.json
 }
 ```
 
+If the `part` key/value pair is absent from a filename, the image SHOULD be a 
+magnitude image.
+
 #### The `run` entity
 
 If several scans of the same modality are acquired they MUST be indexed with a
@@ -480,7 +497,11 @@ fields specific to anatomical scans:
 
 ##### Legacy suffixes (to be deprecated)
 
-Some suffixes that were available in versions of the specification prior to 1.x.x. have been identified as legacy suffixes. The legacy sufficies generate inconsistencies and/or ambiguities with additional sufficies added in version 1.x.x and so are therefore not recommended for use in new datasets. They remain valid sufficies to maintain backwards compatibility with earlier datasets.

+Some suffixes that were available in versions of the specification prior to
+1.x.x. have been identified as legacy suffixes. The legacy sufficies generate
+inconsistencies and/or ambiguities with additional sufficies added in version
+1.x.x and so are therefore not recommended for use in new datasets. They are,
+however, still valid sufixxes, to maintain backwards compatibility.

 
 The following suffixes are valid, but SHOULD NOT be used for new BIDS compatible datasets (created after version 1.x.x.):
 
@@ -576,8 +597,21 @@ JSON file.
 
 | Field name     | Definition                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
 |-----------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| RepetitionTime | REQUIRED. The time in seconds between the beginning of an acquisition of one volume and the beginning of acquisition of the volume following it (TR). When used in the context of functional acquisitions this parameter best corresponds to [DICOM Tag 0020,0110](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0020,0110)): the "time delta between images in a dynamic of functional set of images" but may be found in [DICOM Tag 0018, 0080](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)): "the period of time in msec between the beginning of a pulse sequence and the beginning of the succeeding (essentially identical) pulse sequence". This definition includes time between scans (when no data has been acquired) in case of sparse acquisition schemes. This value MUST be consistent with the '`pixdim[4]`' field (after accounting for units stored in '`xyzt_units`' field) in the NIfTI header. This field is mutually exclusive with `VolumeTiming`. |
-| VolumeTiming   | REQUIRED. The time at which each volume was acquired during the acquisition. It is described using a list of times (in JSON format) referring to the onset of each volume in the BOLD series. The list must have the same length as the BOLD series, and the values must be non-negative and monotonically increasing. This field is mutually exclusive with `RepetitionTime` and `DelayTime`. If defined, this requires acquisition time (TA) be defined via either `SliceTiming` or `AcquisitionDuration` be defined.                                        |
+| RepetitionTime | REQUIRED. The time in seconds between the beginning of an
+acquisition of one volume and the beginning of acquisition of the volume
+following it (TR). When used in the context of functional acquisitions this
+parameter best corresponds to
+[DICOM Tag 0020,0110](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0020,0110)):
+the "time delta between images in a dynamic of functional set of images" but
+may also be found in [DICOM Tag 0018, 0080](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)):
+"the period of time in msec between the beginning of a pulse sequence and
+the beginning of the succeeding (essentially identical) pulse sequence".
+This definition includes time between scans (when no data has been acquired)
+in case of sparse acquisition schemes. This value MUST be consistent with the
+'`pixdim[4]`' field (after accounting for units stored in '`xyzt_units`' field)
+in the NIfTI header. This field is mutually exclusive with `VolumeTiming`. |
+| VolumeTiming   | REQUIRED. The time at which each volume was acquired during the
+acquisition. It is described using a list of times (in JSON format) referring to the onset of each volume in the BOLD series. The list must have the same length as the BOLD series, and the values must be non-negative and monotonically increasing. This field is mutually exclusive with `RepetitionTime` and `DelayTime`. If defined, this requires acquisition time (TA) be defined via either `SliceTiming` or `AcquisitionDuration` be defined.                                        |
 | TaskName       | REQUIRED. Name of the task. No two tasks should have the same name. The task label included in the file name is derived from this TaskName field by removing all non-alphanumeric (`[a-zA-Z0-9]`) characters. For example TaskName `faces n-back` will correspond to task label `facesnback`. A RECOMMENDED convention is to name resting state task using labels beginning with `rest`.                                                                                                                                                                       |
 
 For the fields described above and in the following section, the term "Volume"

From cd8c7e074169729face73f5791d3e0e714f2a8d1 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Fri, 19 Jun 2020 08:22:54 -0400
Subject: [PATCH 68/76] Insert entity table for anatomy imaging data

---
 mkdocs.yml                                    |   3 +-
 src/99-appendices/04-entity-table.md          |  24 ++--
 src/99-appendices/09-BEP001-conversion-tmp.md | 119 ------------------
 src/99-appendices/{10-qmri.md => 09-qmri.md}  |   0
 4 files changed, 16 insertions(+), 130 deletions(-)
 delete mode 100644 src/99-appendices/09-BEP001-conversion-tmp.md
 rename src/99-appendices/{10-qmri.md => 09-qmri.md} (100%)

diff --git a/mkdocs.yml b/mkdocs.yml
index a67345e019..60f0353ac2 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -48,8 +48,7 @@ nav:
         - MEG file formats: 99-appendices/06-meg-file-formats.md
         - MEG systems: 99-appendices/07-meg-systems.md
         - Coordinate systems: 99-appendices/08-coordinate-systems.md
-        - qMRI: 99-appendices/10-qmri.md
-        - BEP001: 99-appendices/09-BEP001-conversion-tmp.md
+        - qMRI: 99-appendices/09-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/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 54bd9abb95..5bb604100e 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -13,15 +13,6 @@ A general introduction to entities is given in the section on
 | Entity                                                                                         | Subject       | Session       | Task           | Acquisition   | Contrast Enhancing Agent | Reconstruction | Phase-Encoding Direction | Run           | Corresponding modality | Echo           | Recording           | Processed (on device) | Space           | Split           |
 | :--------------------------------------------------------------------------------------------- | :------------ | :------------ | :------------- | :------------ | :----------------------- | :------------- | :----------------------- | :------------ | :--------------------- | :------------- | :------------------ | :-------------------- | :---------------| :-------------- |
 | Format                                                                                         | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`             | `rec-<label>`  | `dir-<label>`            | `run-<index>` | `mod-<label>`          | `echo-<index>` | `recording-<label>` | `proc-<label>`        | `space-<label>` | `split-<index>` |
-| anat<br>(T1w T2w  PDw T2starw  FLASH inplaneT1  inplaneT2)                                                    | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        |                |              |                |                        | OPTIONAL           |                     |                |                 |
-| anat<br>(defacemask)                                                                                          | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      | OPTIONAL               |                |              |                |                        |                    |                     |                |                 |
-| anat<br>(T1map T2map T2starmap R1map R2map R2starmap PDmap MTRmap MTsat UNIT1 T1rho MWFmap PDT2map B1plusmap) | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        |                |              |                |                        |                    |                     |                |                 |
-| anat<br>(MESE MGRE)                                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        | REQUIRED       |              |                |                        | OPTIONAL           |                     |                |                 |
-| anat<br>(VFA B1DAM)                                                                                           | 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)                                                                                             | REQURED       | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        | OPTIONAL       | REQUIRED     |                | REQUIRED               | OPTIONAL           |                     |                |                 |
-| anat<br>(MTR)                                                                                                 | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        |                |              |                | REQUIRED               | OPTIONAL           |                     |                |                 |
-| anat<br>(IRT1)                                                                                                | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        |                |              | REQUIRED       |                        | OPTIONAL           |                     |                |                 |
 | func<br>(bold cbv phase sbref events)                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     |                       |                 |                 |
 | func<br>(physio stim)                                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          | OPTIONAL       |                          | OPTIONAL      |                        |                | OPTIONAL            | OPTIONAL              |                 |                 |
 | dwi<br>(dwi bvec bval)                                                                         | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                | OPTIONAL                 | OPTIONAL      |                        |                |                     |                       |                 |                 |
@@ -37,3 +28,18 @@ A general introduction to entities is given in the section on
 | photo<br>(meg/eeg/ieeg)                                                                        | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          |               |                        |                |                     |                       |                 |                 |        
 | electrodes<br>(eeg/ieeg)                                                                       | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          |               |                        |                |                     |                       | OPTIONAL        |                 |
 | events<br>(meg/eeg/ieeg)                                                                       | REQUIRED      | OPTIONAL      | REQUIRED       |               |                          |                |                          | OPTIONAL      |                        |                |                     |                       |                 |                 |        
+
+## Entity table for anatomy imaging data
+
+| Entity                                                                                                     | Subject       | Session       | Task           | Acquisition   | Contrast Enhancing Agent | Reconstruction | Phase-Encoding Direction | Run           | Corresponding Modality | Echo           | Flip Angle   | Inversion Time | Magnetization Transfer | Part               | Recording           | Processed      | Space           |
+|------------------------------------------------------------------------------------------------------------|---------------|---------------|----------------|---------------|--------------------------|----------------|--------------------------|---------------|------------------------|----------------|--------------|----------------|------------------------|--------------------|---------------------|----------------|-----------------|
+| Format                                                                                                     | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`             | `rec-<label>`  | `dir-<label>`            | `run-<index>` | `mod-<suffix>`         | `echo-<index>` | `fa-<index>` | `inv-<index>`  | `mt-<on/off>`          | `part-<label>` | `recording-<label>` | `proc-<label>` | `space-<label>` |
+| anat (T1w T2w  PDw T2starw  FLASH inplaneT1  inplaneT2)                                                    | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        |                |              |                |                        | OPTIONAL           |                     |                |                 |
+| anat (defacemask)                                                                                          | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      | OPTIONAL               |                |              |                |                        |                    |                     |                |                 |
+| anat (T1map T2map T2starmap R1map R2map R2starmap PDmap MTRmap MTsat UNIT1 T1rho MWFmap PDT2map B1plusmap) | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        |                |              |                |                        |                    |                     |                |                 |
+| anat (MESE MGRE)                                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        | REQUIRED       |              |                |                        | OPTIONAL           |                     |                |                 |
+| anat (VFA)                                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        |                | REQUIRED     |                |                        | OPTIONAL           |                     |                |                 |
+| anat (MP2RAGE)                                                                                             | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        | OPTIONAL       | REQUIRED     | REQUIRED       |                        | OPTIONAL           |                     |                |                 |
+| anat (MPM MTS)                                                                                             | REQURED       | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        | OPTIONAL       | REQUIRED     |                | REQUIRED               | OPTIONAL           |                     |                |                 |
+| anat (MTR)                                                                                                 | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        |                |              |                | REQUIRED               | OPTIONAL           |                     |                |                 |
+| anat (IRT1)                                                                                                | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          | OPTIONAL      |                        |                |              | REQUIRED       |                        | OPTIONAL           |                     |                |                 |
\ No newline at end of file
diff --git a/src/99-appendices/09-BEP001-conversion-tmp.md b/src/99-appendices/09-BEP001-conversion-tmp.md
deleted file mode 100644
index 875c3d2404..0000000000
--- a/src/99-appendices/09-BEP001-conversion-tmp.md
+++ /dev/null
@@ -1,119 +0,0 @@
-> :warning: This `temporary` appendix is intended to provide a conversion guideline between
-different versions of BEP001. 
-
-## Changes to `acq` entity
-
-### Previous convention
-
-In the previous version, the `acq` entity was used to define custom `tags` that 
-specify different combinations of multiple entities:
-
-| Grouping suffix | Labels           | Respective metadata fields and values   |
-|-------------|------------------|------------------------------|
-| MTR         | `MTon`, `MToff`      | MTState [`On`, `Off`] |
-| MTS         | `MTon`, `MToff`, `T1w` | MTstate [`On`,`Off`,`Off`], FlipAngle [`lower`,`lower`,`higher`] |
-| MPM         | `MTon`, `MToff`, `T1w` | MTstate [`On`,`Off`,`Off`], FlipAngle [`lower`,`lower`,`higher`] |
-
-The table above uses `acq` entity to this end for `MTS` and `MTR` by combining 
-two entities (`fa` and non-existing `mt`). 
-
-### New convention
-
-As the previous convention imposed a specific role to a free-from entity, the 
-solution was not ideal and did not receive positive feedback.
-
-To free `acq` tag, we introduced a new entity `mt`, for the suffixes described in BEP001 so far. This limitation applied to `MTR`, `MTS` and `MPM` suffixes. 
-
-These entities will appear in the filenames in the following (alphabetical) order: 
-
-`echo` --> `fa` --> `inv` --> `mt` 
-
-#### Changes for MTR
-
-```diff
---- MTState on
-- sub-01_acq-MTon_MTR.nii.gz
-+ sub-01_mt-on_MTR.nii.gz
-
-
---- MTState off
-- sub-01_acq-MToff_MTR.nii.gz
-+ sub-01_mt-off_MTR.nii.gz
-```
-
-#### Changes for MTS
-
-```diff
-
---- MTState on | FlipAngle lower
------- a.k.a MTw
-- sub-01_acq-MTon_MTS.nii.gz
-+ sub-01_fa-1_mt-on_MTS.nii.gz
-
-
---- MTState off | FlipAngle lower
------- a.k.a PDw
-- sub-01_acq-MToff_MTS.nii.gz
-+ sub-01_fa-1_mt-off_MTS.nii.gz
-
-
---- MTState off | FlipAngle higher
------- a.k.a T1w
-- sub-01_acq-T1w_MTS.nii.gz
-+ sub-01_fa-2_mt-off_MTS.nii.gz
-```
-
-> :warning: **fa-2 > fa-1**
-
-#### Changes for MPM
-```diff
-
---- MTState on | FlipAngle lower | Echo 1
------- a.k.a MTw
-- sub-01_echo-1_acq-MTon_MPM.nii.gz
-+ sub-01_echo-1_fa-1_mt-on_MPM.nii.gz
-
-
---- MTState off | FlipAngle lower | Echo 1
------- a.k.a PDw
-- sub-01_echo-1_acq-MToff_MPM.nii.gz
-+ sub-01_echo-1_fa-1_mt-off_MPM.nii.gz
-
-
---- MTState off | FlipAngle higher | Echo 1
------- a.k.a T1w
-- sub-01_echo-1_acq-T1w_MPM.nii.gz
-+ sub-01_echo-1_fa-2_mt-off_MPM.nii.gz
-```
-
-> :warning: **fa-2 > fa-1**
-
-### Other considerations
-
-#### 1) `RepetitionTime` --> `RepetitionTimeExcitation`
-
-Please use `RepetitionTimeExcitation` for `TR` in anatomical imaging data json files. 
-
-For anatomical acquisitions with multiple readout blocks within a `TR` (e.g. `MP2RAGE`), `RepetitionTimeExcitation` is used along with `RepetitionTimePreparation`.  
-
-#### 2) Ordering of the `metadata` values with respect to the `index` 
-
-##### Ascending order indexing 
-|entity| respective `EchoTime` value in JSON|
-|-------------|------------------|
-|echo-1|          0.005        | 
-|echo-2|          0.010        | 
-|echo-3|          0.015        | 
-etc. 
-
-|entity| respective `FlipAngle` value in JSON|
-|-------------|------------------|
-|fa-1|          5        |
-|fa-2|          25       |
-etc.
-
-> :warning: Indexes MUST correspond to the same value throughout the dataset. For example, `fa-2` MUST NOT point to `FlipAngle = 5` for `echo-1` and to something else (e.g. `FlipAngle = 25`) for `echo-2`.
-
-#### 3) `index` numeric format 
-
-Use format `%03d` (`001`,`002`,etc) instead of `%d` (`1`,`2`,etc.) for better listing. 
diff --git a/src/99-appendices/10-qmri.md b/src/99-appendices/09-qmri.md
similarity index 100%
rename from src/99-appendices/10-qmri.md
rename to src/99-appendices/09-qmri.md

From 6bdae74de3a53005e43fe502818ef404161d55db Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Fri, 19 Jun 2020 08:27:39 -0400
Subject: [PATCH 69/76] Fix rtd

---
 .../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 3026112643..9396cb6d9e 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
@@ -322,8 +322,8 @@ expand or to modify the following table.
 | Longutidunal relaxation in rotating frame (T1 rho) map | T1rho     | Parametric   | In seconds (s). T1-rho maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ N/A                                                                                                                                             |
 | Myelin water fraction map                              | MWFmap    | Parametric   | In percentage (%). MWF maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`                                                                                                                                          |
 | Combined PD/T2 map                                     | PDT2map   | Parametric   | In arbitrary units (a.u.). Combined PD/T2 maps are REQUIRED to use this suffix irrespective of the method they are related to. N/A                                                                                                                                                   |
-| RF transmit field map                                  | TB1map | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/10-qmri.md) for associated inputs and further details                                                                     |
-| RF receive sensitivity map                                  | RB1map | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/10-qmri.md) for associated inputs and further details                                                                     |
+| RF transmit field map                                  | TB1map | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/09-qmri.md) for associated inputs and further details                                                                     |
+| RF receive sensitivity map                                  | RB1map | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/09-qmri.md) for associated inputs and further details                                                                     |
 | Observed signal amplitude map                                | S0map | Parametric   | In arbitrary units (a.u.). For a multi-echo sequence, S0 maps index the baseline signal before exponential (T2\*) 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 REQUIRED to use this suffix irrespective of the method they are related to. _Associated suffixes:_ T2starmap.       |
 | Quantitative susceptibility map (QSM)                   | Chimap | Parametric   | In parts per million (ppm). QSM allows for determining the underlying magnetic susceptibility of tissue (Chi).  Chi-maps are usually constructed from the phase images of GRE sequences. Chi-maps are quantitative and are reconstructed by solving the magnetic field to susceptibility source inverse problem ([Wang & Liu, 2014](https://onlinelibrary.wiley.com/doi/10.1002/mrm.25358)). |
 
@@ -777,7 +777,7 @@ acquired with EPI sequences.
 
 B1<sup>+</sup> and B1<sup>-</sup>  maps are mostly used in anatomical imaging, especially
 in quantitative MRI applications. Further information about these radiofrequency (RF)
-field maps are available in the [qMRI appendix](../99-appendices/10-qmri.md).
+field maps are available in the [qMRI appendix](../99-appendices/09-qmri.md).
 
 #### B0 fieldmaps
 Data acquired to correct for B0 inhomogeneities can come in different forms. The

From 173ebc00cb2e4159f7748bad6d6215e114d864bc Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Mon, 22 Jun 2020 06:30:09 -0400
Subject: [PATCH 70/76] Fix table rows

---
 .../01-magnetic-resonance-imaging-data.md       | 17 ++---------------
 1 file changed, 2 insertions(+), 15 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 9396cb6d9e..ae299abd04 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
@@ -597,21 +597,8 @@ JSON file.
 
 | Field name     | Definition                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
 |-----------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| RepetitionTime | REQUIRED. The time in seconds between the beginning of an
-acquisition of one volume and the beginning of acquisition of the volume
-following it (TR). When used in the context of functional acquisitions this
-parameter best corresponds to
-[DICOM Tag 0020,0110](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0020,0110)):
-the "time delta between images in a dynamic of functional set of images" but
-may also be found in [DICOM Tag 0018, 0080](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)):
-"the period of time in msec between the beginning of a pulse sequence and
-the beginning of the succeeding (essentially identical) pulse sequence".
-This definition includes time between scans (when no data has been acquired)
-in case of sparse acquisition schemes. This value MUST be consistent with the
-'`pixdim[4]`' field (after accounting for units stored in '`xyzt_units`' field)
-in the NIfTI header. This field is mutually exclusive with `VolumeTiming`. |
-| VolumeTiming   | REQUIRED. The time at which each volume was acquired during the
-acquisition. It is described using a list of times (in JSON format) referring to the onset of each volume in the BOLD series. The list must have the same length as the BOLD series, and the values must be non-negative and monotonically increasing. This field is mutually exclusive with `RepetitionTime` and `DelayTime`. If defined, this requires acquisition time (TA) be defined via either `SliceTiming` or `AcquisitionDuration` be defined.                                        |
+| RepetitionTime | REQUIRED. The time in seconds between the beginning of an acquisition of one volume and the beginning of acquisition of the volume following it (TR). When used in the context of functional acquisitions this parameter best corresponds to [DICOM Tag 0020,0110](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0020,0110)): the "time delta between images in a dynamic of functional set of images" but may also be found in [DICOM Tag 0018, 0080](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)): "the period of time in msec between the beginning of a pulse sequence and the beginning of the succeeding (essentially identical) pulse sequence". This definition includes time between scans (when no data has been acquired) in case of sparse acquisition schemes. This value MUST be consistent with the '`pixdim[4]`' field (after accounting for units stored in '`xyzt_units`' field) in the NIfTI header. This field is mutually exclusive with `VolumeTiming`. |
+| VolumeTiming   | REQUIRED. The time at which each volume was acquired during the acquisition. It is described using a list of times (in JSON format) referring to the onset of each volume in the BOLD series. The list must have the same length as the BOLD series, and the values must be non-negative and monotonically increasing. This field is mutually exclusive with `RepetitionTime` and `DelayTime`. If defined, this requires acquisition time (TA) be defined via either `SliceTiming` or `AcquisitionDuration` be defined.                                        |
 | TaskName       | REQUIRED. Name of the task. No two tasks should have the same name. The task label included in the file name is derived from this TaskName field by removing all non-alphanumeric (`[a-zA-Z0-9]`) characters. For example TaskName `faces n-back` will correspond to task label `facesnback`. A RECOMMENDED convention is to name resting state task using labels beginning with `rest`.                                                                                                                                                                       |
 
 For the fields described above and in the following section, the term "Volume"

From a446679d423020c5496a4b1c8ea958641ac438a5 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Mon, 22 Jun 2020 06:39:14 -0400
Subject: [PATCH 71/76] Replace placeholder text

---
 .../01-magnetic-resonance-imaging-data.md              | 10 +++++-----
 1 file changed, 5 insertions(+), 5 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 ae299abd04..a6bb7f18e4 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
@@ -186,7 +186,7 @@ imaging data, the `_<suffix>` entity can be used in one of three ways:
 3. Quantitative MRI (qMRI) map suffixes
 
 This distinction was added to the specification on acceptance of the BEP001 
-proposal in version `1.x.x`. However, as a result, some  suffixes that were introduced
+proposal in version `1.4.0`. However, as a result, some  suffixes that were introduced
 into BIDS at an earlier point time are inconsistent with this typology: for example 
 because they are linked to a readout-sequence rather than a contrast, or because 
 they don't clearly distinguish between a quantitative map or a contrast-weighted 
@@ -198,7 +198,7 @@ These can be found in the [legacy suffixes](#legacy-suffixes) subsection.
 
 Previous versions of the specification used the term `modality_label` instead of 
 `_suffix` to represent this entity. The change in term was introduced in version 
-`1.x.x.` to accodomate a broad definition of anatomical imaging applications.
+`1.4.0.` to accodomate a broad definition of anatomical imaging applications.
 
 ##### Conventional MRI suffixes
 
@@ -498,12 +498,12 @@ fields specific to anatomical scans:
 ##### Legacy suffixes (to be deprecated)
 
 Some suffixes that were available in versions of the specification prior to
-1.x.x. have been identified as legacy suffixes. The legacy sufficies generate
+1.4.0. have been identified as legacy suffixes. The legacy sufficies generate
 inconsistencies and/or ambiguities with additional sufficies added in version
-1.x.x and so are therefore not recommended for use in new datasets. They are,
+1.4.0 and so are therefore not recommended for use in new datasets. They are,
 however, still valid sufixxes, to maintain backwards compatibility.

 
-The following suffixes are valid, but SHOULD NOT be used for new BIDS compatible datasets (created after version 1.x.x.):
+The following suffixes are valid, but SHOULD NOT be used for new BIDS compatible datasets (created after version 1.4.0.):
 
 | Name           | Suffix    | Description                                                    | Reason to deprecate                                                                                                                                                                                                                                                                                                                                                                                                |
 |----------------|-----------|----------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

From 349d58b52e83fa0042b90edcd21eeaf470ce52e3 Mon Sep 17 00:00:00 2001
From: agahkarakuzu <agahkarakuzu@gmail.com>
Date: Mon, 22 Jun 2020 06:41:41 -0400
Subject: [PATCH 72/76] 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 a6bb7f18e4..94862a9968 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
@@ -501,7 +501,7 @@ Some suffixes that were available in versions of the specification prior to
 1.4.0. have been identified as legacy suffixes. The legacy sufficies generate
 inconsistencies and/or ambiguities with additional sufficies added in version
 1.4.0 and so are therefore not recommended for use in new datasets. They are,
-however, still valid sufixxes, to maintain backwards compatibility.

+however, still valid sufixes, to maintain backwards compatibility.
 
 The following suffixes are valid, but SHOULD NOT be used for new BIDS compatible datasets (created after version 1.4.0.):
 

From 10a6c6a0e8ef42284bab44039c7dec121de7aefc Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Tue, 23 Jun 2020 14:03:29 +0200
Subject: [PATCH 73/76] Update
 src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Changes _are_

Co-authored-by: Thomas Nichols <nicholst@users.noreply.github.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 94862a9968..e5cbb2f680 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
@@ -304,7 +304,7 @@ have to be stored separately in each `.json`-sidecar file.
 Denotes the parameter contained within an individual file of a
 quantitative parametric image.
 
-Changes to the specification is REQUIRED to
+Changes to the specification are REQUIRED to
 expand or to modify the following table.
 
 | Name                                                   | _suffix   | _suffix type | Description                                                                                                                                                                                                                                                                          |

From 3b4be52b17eeb19bd882120be60cca48a91291a2 Mon Sep 17 00:00:00 2001
From: Kirstie Whitaker <kw401@cam.ac.uk>
Date: Wed, 24 Jun 2020 10:38:19 +0100
Subject: [PATCH 74/76] Apply suggestions from code review

Co-authored-by: Thomas Nichols <nicholst@users.noreply.github.com>
Co-authored-by: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
---
 .../01-magnetic-resonance-imaging-data.md            | 12 ++++++------
 1 file changed, 6 insertions(+), 6 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 e5cbb2f680..da96d55d11 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
@@ -202,7 +202,7 @@ Previous versions of the specification used the term `modality_label` instead of
 
 ##### Conventional MRI suffixes
 
-**Function:**
+**Purpose:**
 
 Denotes the type of the predominant contrast conveyed by an individual file of
 a conventional anatomical image.
@@ -252,7 +252,7 @@ sub-01_mod-T1w_defacemask.json
 ```
 ##### Grouping suffixes
 
-**Function:**
+**Purpose:**
 
 Files that belong to a **grouped scan collection** are part of a single scan
 protocol that acquires multiple images with  similar acquisition parameters
@@ -345,7 +345,7 @@ description of the `T1map` suffix requires the parameter to be in seconds (s).
 
 #### The `part` entity
 
-This entity shall be used to indicate which component of the complex representation
+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](https://dicom.innolitics.com/ciods/enhanced-mr-image/enhanced-mr-image/00089208).
@@ -498,10 +498,10 @@ fields specific to anatomical scans:
 ##### Legacy suffixes (to be deprecated)
 
 Some suffixes that were available in versions of the specification prior to
-1.4.0. have been identified as legacy suffixes. The legacy sufficies generate
-inconsistencies and/or ambiguities with additional sufficies added in version
+1.4.0. have been identified as legacy suffixes. The legacy suffixes generate
+inconsistencies and/or ambiguities with additional suffixes added in version
 1.4.0 and so are therefore not recommended for use in new datasets. They are,
-however, still valid sufixes, to maintain backwards compatibility.
+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 1.4.0.):
 

From 82c9883cebe66fdd579b2c01c39cd91ea7462336 Mon Sep 17 00:00:00 2001
From: Kirstie Whitaker <kw401@cam.ac.uk>
Date: Wed, 24 Jun 2020 15:15:28 +0100
Subject: [PATCH 75/76] Apply suggestions from code review

Thank you @tsalo!

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
---
 .../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 da96d55d11..0fe812c500 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
@@ -136,7 +136,7 @@ information about (brain) anatomy, but differ by the nature of the data they con
 This type is most commonly used in neuroimaging applications.
 2. a group of images acquired within a single protocol for the purpose of improving contrast 
 characteristics (e.g., a set of multi-echo anatomical GRE images) or calculating quantitative maps
-(e.g. four 3D volumes provided as an input to an MP2RAGE calculation) 
+(e.g. four 3D volumes provided as an input to an MP2RAGE calculation). 
 3. a quantitative map of which the intensities are put on an absolute scales (e.g., seconds for a T1 map).
 These images are generally produced by some mathematical operation on images from class 2.
 
@@ -144,7 +144,7 @@ These images are generally produced by some mathematical operation on images fro
 
 Anatomical images of this type typically refer to a volumetric high-resolution 
 dataset, representing the measured MRI signal in an arbitrary scale of "gray
-shades". Contrast factor of these grayscale images depend on the relative contribution
+shades". Contrast factor of these grayscale images depends on the relative contribution
 of inherent tissue parameters (e.g. `T1`, `T2` and `PD`) to the measured signal. 
 
 Contribution weights of these parameters are determined by the type of acquisition
@@ -311,7 +311,7 @@ expand or to modify the following table.
 |--------------------------------------------------------|-----------|--------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
 | Longitudinal relaxation time map                       | T1map     | Parametric   | In seconds (s). T1 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `VFA`, `IRT1`, `MP2RAGE`, `MTS`,`MPM`. 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     | Parametric   | In seconds (s). T2 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`, `MPM`                                                                                                                                       |
-| Observed transverse relaxation time map                | T2starmap | Parametric   | In seconds (s). T2\* maps are REQUIRED to use this suffix irrespective of the method they are related to._Can be generated from:_ `MEGRE`, `MPM`                                                                                                                                      |
+| Observed transverse relaxation time map                | T2starmap | Parametric   | In seconds (s). T2\* maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MEGRE`, `MPM`                                                                                                                                     |
 | Longitudinal relaxation rate map                       | R1map     | Parametric   | In seconds-1 (1/s). R1 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `VFA`, `IRT1`, `MP2RAGE`, `MTS`, `MPM`                                                                                                           |
 | True transverse relaxation rate map                    | R2map     | Parametric   | In seconds-1 (1/s). R2 maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`, `MPM`                                                                                                                                  |
 | Observed transverse relaxation rate map                | R2starmap | Parametric   | In seconds-1 (1/s). R2\* maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_`MEGRE`, `MPM`                                                                                                                                 |

From 87473ae9a932d7138ec5c4def77e31e5fd35e541 Mon Sep 17 00:00:00 2001
From: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Date: Wed, 24 Jun 2020 16:27:52 +0200
Subject: [PATCH 76/76] Update
 src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Spelling mistake fixed by @tsalo

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 0fe812c500..8721913ad8 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
@@ -319,7 +319,7 @@ expand or to modify the following table.
 | Magnetization transfer ratio map                       | MTRmap    | Parametric   | In percentage (%). MTR maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MTR`                                                                                                                                           |
 | Magnetization transfer saturation index map            | MTsat     | Parametric   | In arbitrary units (a.u.). MTsat maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MTS`, `MPM`                                                                                                                          |
 | Homogeneous (flat) T1-weighted image by MP2RAGE                 | UNIT1     | Parametric   | 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` _Can be generated from:_ `MP2RAGE`                                                                                                                             |
-| Longutidunal relaxation in rotating frame (T1 rho) map | T1rho     | Parametric   | In seconds (s). T1-rho maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ N/A                                                                                                                                             |
+| Longitudinal relaxation in rotating frame (T1 rho) map | T1rho     | Parametric   | In seconds (s). T1-rho maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ N/A                                                                                                                                             |
 | Myelin water fraction map                              | MWFmap    | Parametric   | In percentage (%). MWF maps are REQUIRED to use this suffix irrespective of the method they are related to. _Can be generated from:_ `MESE`                                                                                                                                          |
 | Combined PD/T2 map                                     | PDT2map   | Parametric   | In arbitrary units (a.u.). Combined PD/T2 maps are REQUIRED to use this suffix irrespective of the method they are related to. N/A                                                                                                                                                   |
 | RF transmit field map                                  | TB1map | Parametric   | 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. Please see the [qMRI appendix](../99-appendices/09-qmri.md) for associated inputs and further details                                                                     |