[ENH] Bep 009: Positron Emission Tomography

mkdocs.yml

@@ -35,6 +35,7 @@ nav:
         - Physiological and other continuous recordings: 04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
         - Behavioral experiments (with no neural recordings): 04-modality-specific-files/07-behavioral-experiments.md
         - Genetic Descriptor: 04-modality-specific-files/08-genetic-descriptor.md
+        - Positron Emission Tomography: 04-modality-specific-files/09-positron-emission-tomography.md
       - Derivatives:
         - BIDS Derivatives: 05-derivatives/01-introduction.md
         - Common data types and metadata: 05-derivatives/02-common-data-types.md
@@ -54,6 +55,7 @@ nav:
         - File collections: 99-appendices/10-file-collections.md
         - Quantitative MRI: 99-appendices/11-qmri.md
         - Arterial Spin Labeling: 99-appendices/12-arterial-spin-labeling.md
+        - Cross modality correspondence: 99-appendices/13-cross-modality-correspondence.md
       - Changelog: CHANGES.md
     - The BIDS Starter Kit:
       - GitHub repository: https://github.com/bids-standard/bids-starter-kit

src/01-introduction.md

@@ -111,6 +111,18 @@ For example:
     Scientific Data, 5 (180110).
     [doi:10.1038/sdata.2018.110](https://doi.org/10.1038/sdata.2018.110)
 
+#### PET
+
+-   Knudsen GM, Ganz M, Appelhoff S, Boellaard R, Bormans G, Carson RE, Catana C,
+    Doudet D, Gee AD, Greve DN, Gunn RN, Halldin C, Herscovitch P, Huang H, Keller SH,
+    Lammertsma AA, Lanzenberger R, Liow JS, Lohith TG, Lubberink M, Lyoo CH, Mann JJ,
+    Matheson GJ, Nichols TE, Nørgaard M, Ogden T, Parsey R, Pike VW, Price J, Rizzo G,
+    Rosa-Neto P, Schain M, Scott PJH, Searle G, Slifstein M, Suhara T, Talbot PS,
+    Thomas A, Veronese M, Wong DF, Yaqub M, Zanderigo F, Zoghbi S, Innis RB. (2020).
+    **Guidelines for Content and Format of PET Brain Data in Publications and in Archives: A Consensus Paper**.
+    Journal of Cerebral Blood Flow and Metabolism, 2020 Aug; 40(8): 1576-1585.
+    [doi:10.1177/0271678X20905433](https://doi.org/10.1177/0271678X20905433)
+
 #### Genetics
 
 -   Clara Moreau, Martineau Jean-Louis, Ross Blair, Christopher Markiewicz, Jessica Turner,

src/02-common-principles.md

@@ -28,6 +28,9 @@ misunderstanding we clarify them here.
     sessions is appropriate when several identical or similar data acquisitions
     are planned and performed on all -or most- subjects, often in the case of
     some intervention between sessions (for example, training).
+    In the [PET](04-modality-specific-files/09-positron-emission-tomography.md)
+    context, a session may also indicate a group of related scans,
+    taken in one or more visits.
 
 1.  **Data acquisition** - a continuous uninterrupted block of time during which
     a brain scanning instrument was acquiring data according to particular
@@ -73,6 +76,13 @@ misunderstanding we clarify them here.
     acquisition parameters and task (however events can change from run to run
     due to different subject response or randomized nature of the stimuli). Run
     is a synonym of a data acquisition.
+    Note that "uninterrupted" may look different by modality due to the nature of the
+    recording.
+    For example, in [MRI](04-modality-specific-files/01-magnetic-resonance-imaging-data.md)
+    or [MEG] (04-modality-specific-files/02-magnetoencephalography.md),
+    if a subject leaves the scanner, the acquisition must be restarted.
+    For some types of [PET](04-modality-specific-files/09-positron-emission-tomography.md) acquisitions,
+    a subject may leave and re-enter the scanner without interrupting the scan.
 
 1.  **Modality** - the category of brain data recorded by a file.
     For MRI data, different pulse sequences are considered distinct modalities,

src/99-appendices/04-entity-table.md

@@ -29,6 +29,10 @@ while entity definitions are in [Appendix IX](09-entities.md).
 
 {{ MACROS___make_entity_table(datatypes=["meg"], auxdatatypes=["channels", "events", "photo"]) }}
 
+## Positron Emission Tomography (PET)
+
+{{ MACROS___make_entity_table(datatypes=["pet"]) }}
+
 ## Behavioral Data
 
 {{ MACROS___make_entity_table(datatypes=["beh"], auxdatatypes=[]) }}

src/99-appendices/13-cross-modality-correspondence.md

@@ -0,0 +1,14 @@
+# Appendix XIII: Cross modality correspondence
+
+## PET-MRI correspondence
+
+When sharing MRI data alongside with PET data,
+please pay specific attention to the format the MR images are in.
+It is important to note whether the MR images have been unwarped
+in order to correct for gradient non-linearities,
+indicated by the `NonlinearGradientCorrection` metadata field
+(see [Magnetic Resonance Imaging Data - Sequence Specifics](../04-modality-specific-files/01-magnetic-resonance-imaging-data.md#sequence-specifics)).
+The reason for this is that the MRI needs to be corrected for nonlinear gradients
+in order to fit the accompanying PET scans for co-registration
+(Knudsen et al. 2020, [doi:10.1177/0271678X20905433](https://doi.org/10.1177/0271678X20905433);
+Norgaard et al. 2019, [doi:10.1016/j.neuroimage.2019.05.055](https://doi.org/10.1016/j.neuroimage.2019.05.055)).

src/schema/datatypes/pet.yaml

@@ -0,0 +1,42 @@
+---
+# PET recordings
+- suffixes:
+    - pet
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    subject: required
+    session: optional
+    task: optional
+    tracer: optional
+    reconstruction: optional
+    run: optional
+# Blood recordings
+- suffixes:
+    - blood
+  extensions:
+    - .tsv
+    - .json
+  entities:
+    subject: required
+    session: optional
+    task: optional
+    tracer: optional
+    reconstruction: optional
+    run: optional
+    recording: required
+# Events
+- suffixes:
+    - events
+  extensions:
+    - .tsv
+    - .json
+  entities:
+    subject: required
+    session: optional
+    task: required
+    tracer: optional
+    reconstruction: optional
+    run: optional

src/schema/entities.yaml

@@ -62,9 +62,18 @@ ceagent:
     The `ce-<label>` key/value can be used to distinguish
     sequences using different contrast enhanced images.
     The label is the name of the contrast agent.
-    The key `ContrastBolusIngredient` MAY be also be added in the JSON file,
+    The key `ContrastBolusIngredient` MAY also be added in the JSON file,
     with the same label.
   format: label
+tracer:
+  name: Tracer
+  entity: trc
+  description: |
+    The `trc-<label>` key/value can be used to distinguish
+    sequences using different tracers.
+    The key `TracerName` MUST also be included in the associated JSON file,
+    although the label may be different.
+  format: label
 reconstruction:
   name: Reconstruction
   entity: rec

src/schema/modalities.yaml

@@ -23,3 +23,7 @@ beh:
   name: Behavioral experiments
   datatypes:
     - beh
+pet:
+  name: Positron Emission Tomography
+  datatypes:
+    - pet