[FIX] Data formats clarification

.all-contributorsrc

@@ -3214,6 +3214,14 @@
             ],
             "login": "étienne_bergeron",
             "name": "Étienne Bergeron"
+        },
+        {
+            "contributions": [
+                "code"
+            ],
+            "login": "nbeliy",
+            "name": "Nikita Beliy"
+            "profile": "https://github.com/nbeliy"
         }
     ],
     "contributorsPerLine": 7

src/common-principles.md

@@ -409,20 +409,25 @@ datasets and non-compliant derivatives.
 
 ### Imaging files
 
-All imaging data MUST be stored using the NIfTI file format. We RECOMMEND using
-compressed NIfTI files (.nii.gz), either version 1.0 or 2.0. If using compressed files,
-the gzip header SHOULD lack source filenames and timestamps. Imaging data SHOULD
-be converted to the NIfTI format using a tool that provides as much of the NIfTI
-header information (such as orientation and slice timing information) as
-possible. Since the NIfTI standard offers limited support for the various image
-acquisition parameters available in DICOM files, we RECOMMEND that users provide
-additional meta information extracted from DICOM files in a sidecar JSON file
-(with the same filename as the `.nii[.gz]` file, but with a `.json` extension).
-Extraction of BIDS compatible metadata can be performed using [dcm2niix](https://github.com/rordenlab/dcm2niix)
-and [dicm2nii](https://www.mathworks.com/matlabcentral/fileexchange/42997-xiangruili-dicm2nii)
-DICOM to NIfTI converters. The [BIDS-validator](https://github.com/bids-standard/bids-validator)
-will check for conflicts between the JSON file and the data recorded in the
-NIfTI header.
+All imaging data MUST be stored using BIDS-compatible file format, specified
+in the respective section.
+The conversion from original imaging data format to BIDS-compatible one, if it
+is required, must be performed using a tool that conserves as much of original
+metadata, as possible, at exception of information relative to the participant
+identity, which should not be present in the converted image.
+
+We RECOMMEND that the imaging file will be accompanied with a additional meta
+information extracted from source image and/or external sources in a sidecar
+JSON file.
+If present, sidecar JSON filename MUST be same as as the imaging file, but
+with a `.json` extension.
+
+In some cases BIDS authorize to store compressed imaging files. In such cases
+the compression must be performed using gzip algorithm, and have extension
+`.gz`, for example `sub-123_T1w.nii.gz`.
+The zip header SHOULD lack source filenames and timestamps, this can be
+achieved by using `---name` option of gzip, or first renaming file, and then
+compressing it.
 
 ### Tabular files
 

src/modality-specific-files/magnetic-resonance-imaging-data.md

@@ -1,5 +1,40 @@
 # Magnetic Resonance Imaging
 
+## Data format
+
+All MRI imaging data MUST be stored using the
+[NIfTI-1 or NIFTI-2](https://nifti.nimh.nih.gov/) file format (`.nii`).
+The ANALYZE-7.5 file format (`.hdr`/`.img`), despite being very similar to NIFTI-1,
+is not allowed.
+Imaging data SHOULD be converted to the NIfTI format using a tool that provides
+as much of the NIfTI header information (such as orientation and slice timing
+information) as possible.
+
+We RECOMMEND to use [dcm2niix](https://github.com/rordenlab/dcm2niix)
+to convert source DICOM images to NIFTI-2 file format, as it extracts large
+number of BIDS compatible metadata.
+As alternative,
+[dicm2nii](https://www.mathworks.com/matlabcentral/fileexchange/42997-xiangruili-dicm2nii)
+and
+[spm_dicom_convert](https://github.com/neurodebian/spm12/blob/master/spm_dicom_convert.m)
+from
+[spm12 package](https://github.com/neurodebian/spm12/tree/master) can be used
+for conversion.
+
+Multi-volume acquisitions (for example, 2D slices of anatomical MRI or 3D
+volumes of functional MRI) MUST be concatenated into single image (3D or 4D,
+respectively).
+This can be performed by
+[concat_images](https://nipy.org/nibabel/reference/nibabel.funcs.html) of
+the Nibabel package or by
+[spm_file_merge](https://github.com/spm/spm12/blob/main/spm_file_merge.m).
+
+Due to the important size of MRI imaging data, we RECOMMEND using compressed
+NIfTI files by [gzip](https://www.gzip.org/) algorithm (`.nii.gz`).
+If using compressed files, the gzip header SHOULD lack source filenames and timestamps.
+This can be achieved by using `--no-name` option of gzip, or by first renaming
+original file to BIDS standard and then compressing.
+
 ## Common metadata fields
 
 MR Data described in the following sections share the following RECOMMENDED metadata

src/modality-specific-files/positron-emission-tomography.md

@@ -73,10 +73,43 @@ and a guide for using macros can be found at
    suffixes=["pet", "events", "physio", "stim"])
 }}
 
-PET data MUST be stored in the `pet` directory.
-PET imaging data SHOULD be stored in 4D (or 3D, if only one volume was acquired)
-NIfTI files with the `_pet` suffix.
-Volumes MUST be stored in chronological order (the order they were acquired in).
+### PET data format
+
+All PET imaging data MUST be stored using the
+[NIfTI-1 or NIFTI-2](https://nifti.nimh.nih.gov/) file format (`.nii`).
+The ANALYZE-7.5 file format (`.hdr`/`.img`), despite being very similar to NIFTI-1,
+is not allowed.
+Imaging data SHOULD be converted to the NIfTI format using a tool that provides
+as much of the NIfTI header information (such as orientation and slice timing
+information) as possible.
+
+We RECOMMEND to use [dcm2niix](https://github.com/rordenlab/dcm2niix),
+version v1.0.20220720 or later to convert source DICOM images to NIFTI-2 file format,
+as it extracts a number of PET-specific metadata in BIDS compatible format.
+As alternative,
+[dicm2nii](https://www.mathworks.com/matlabcentral/fileexchange/42997-xiangruili-dicm2nii)
+and
+[spm_dicom_convert](https://github.com/neurodebian/spm12/blob/master/spm_dicom_convert.m)
+from
+[spm12 package](https://github.com/neurodebian/spm12/tree/master) can be used
+for conversion.
+
+Dynamic (multi-volume) PET imaging data SHOULD be stored in 4D,
+in chronological order (the order they were acquired in).
+The concatenation of volumes can be performed by
+[concat_images](https://nipy.org/nibabel/reference/nibabel.funcs.html) of
+the Nibabel package or by
+[spm_file_merge](https://github.com/spm/spm12/blob/main/spm_file_merge.m).
+
+Due to the important size of PET imaging data, we RECOMMEND using compressed
+NIfTI files by [gzip](https://www.gzip.org/) algorithm (`.nii.gz`).
+If using compressed files, the gzip header SHOULD lack source filenames and timestamps.
+This can be achieved by using `--no-name` option of gzip, or by first renaming
+original file to BIDS standard and then compressing.
+
+### PET file naming
+
+PET data MUST be stored in the `pet` directory with `_pet` suffix.
 
 The OPTIONAL [`task-<label>`](../appendices/entities.md#task) is used to
 indicate a task subjects were asked to perform in the scanner.
@@ -129,8 +162,10 @@ the same [`task-<label>`](../appendices/entities.md#task) entity SHOULD be used.
 For further details, see
 [Task (including resting state) imaging data](./magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
 
+<!--
 In addition to the imaging data (`*.nii`) a `_pet.json` sidecar file MUST be provided.
 The included metadata are divided into sections described below.
+-->
 
 ### PET metadata