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How to map DWI images to BIDS filenames #1

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opened 2025-05-06 18:26:09 +00:00 by msz · 0 comments
msz commented 2025-05-06 18:26:09 +00:00
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This is part of the information extracted by Heudiconv while stacking Aachen DICOMs, related to diffusion imaging:

series_id dcm_dir_name series_files protocol_name is_derived
10-Q01_dwi_b1200dir64 Q01_dwi_b1200dir64_10_MR 111 Q01_dwi_b1200dir64 False
11-Q01_dwi_b1200dir64 Q01_dwi_b1200dir64_10_MR 2 Q01_dwi_b1200dir64 True
12-Q01_dwi_b0ref Q01_dwi_b0ref_12_MR 8 Q01_dwi_b0ref False
13-Q01_dwi_mshell Q01_dwi_b0ref_12_MR 156 Q01_dwi_mshell False
14-Q01_dwi_mshell Q01_dwi_mshell_13_MR 2 Q01_dwi_mshell True
15-Q01_dwi_mshell_ref Q01_dwi_mshell_ADC_14_MR 8 Q01_dwi_mshell_ref False

Note: is_derived refers to (0008,0008) ImageType DICOM header field -- apparently either ["ORIGINAL", "PRIMARY", "DIFFUSION", "NONE"] or ["DERIVED", "PRIMARY", "DIFFUSION", "ADC"]

I currently assumed the following naming pattern (numbers refer to the sequence numbers from series_id column above):

10 - sub-P250120_acq-b1200_dwi.nii.gz
11 - discarded
12 - sub-P250120_acq-b1200_sbref.nii.gz
13 - sub-P250120_acq-mshell_dwi.nii.gz
14 - discarded
15 - sub-P250120_acq-mshell_sbref.nii.gz

I am not sure of my choices above. I have the following three questions.

  1. What is the purpose of the DERIVED images? Should they be included in the conversion to BIDS (and if so, what's the naming pattern)?
  2. Is it correct to classify the b0ref (12) and mshell_ref (15) as "single band reference" (sbref suffix)? If yes, then the fact that heudiconv / dcm2niix generates bval and bvec sidecars should be looked into ("The single-band reference image MAY be stored with suffix sbref (for example, dwi/sub-control01_sbref.nii[.gz]) as long as the image has no corresponding gradient information") 1.
  3. Is it expected that the dwi_mshell images (ORIGINAL and DERIVED) are found in Q01_dwi_b0ref_12_MR and Q01_dwi_mshell_13_MR directories respectively?

For reference, here is BIDS spec for diffusion imaging data.

  1. edit 2025-05-08: Heudiconv PR 819 discusses something similar ↩︎

This is part of the information extracted by Heudiconv while stacking Aachen DICOMs, related to diffusion imaging: | series_id | dcm_dir_name | series_files | protocol_name | is_derived | | -------------|----------------------|-----------------|----------------------|----------------| 10-Q01_dwi_b1200dir64 | Q01_dwi_b1200dir64_10_MR | 111 | Q01_dwi_b1200dir64 | False | 11-Q01_dwi_b1200dir64 | Q01_dwi_b1200dir64_10_MR | 2 | Q01_dwi_b1200dir64 | True | 12-Q01_dwi_b0ref| Q01_dwi_b0ref_12_MR | 8 | Q01_dwi_b0ref | False | 13-Q01_dwi_mshell | Q01_dwi_b0ref_12_MR | 156 | Q01_dwi_mshell | False | 14-Q01_dwi_mshell | Q01_dwi_mshell_13_MR | 2 | Q01_dwi_mshell | True | 15-Q01_dwi_mshell_ref | Q01_dwi_mshell_ADC_14_MR | 8 | Q01_dwi_mshell_ref | False | Note: `is_derived` refers to `(0008,0008) ImageType` DICOM header field -- apparently either `["ORIGINAL", "PRIMARY", "DIFFUSION", "NONE"]` or `["DERIVED", "PRIMARY", "DIFFUSION", "ADC"]` I currently assumed the following naming pattern (numbers refer to the sequence numbers from series_id column above): ``` 10 - sub-P250120_acq-b1200_dwi.nii.gz 11 - discarded 12 - sub-P250120_acq-b1200_sbref.nii.gz 13 - sub-P250120_acq-mshell_dwi.nii.gz 14 - discarded 15 - sub-P250120_acq-mshell_sbref.nii.gz ``` I am not sure of my choices above. I have the following three questions. 1. What is the purpose of the DERIVED images? Should they be included in the conversion to BIDS (and if so, what's the naming pattern)? 2. Is it correct to classify the `b0ref` (12) and `mshell_ref` (15) as "single band reference" (sbref suffix)? If yes, then the fact that heudiconv / dcm2niix generates bval and bvec sidecars should be looked into ("The single-band reference image MAY be stored with suffix sbref (for example, dwi/sub-control01_sbref.nii[.gz]) as long as the image has no corresponding gradient information") [^1]. 3. Is it expected that the `dwi_mshell` images (ORIGINAL and DERIVED) are found in `Q01_dwi_b0ref_12_MR` and `Q01_dwi_mshell_13_MR` directories respectively? For reference, here is BIDS spec for [diffusion imaging data](https://bids-specification.readthedocs.io/en/stable/modality-specific-files/magnetic-resonance-imaging-data.html#diffusion-imaging-data). [^1]: edit 2025-05-08: [Heudiconv PR 819](https://github.com/nipy/heudiconv/pull/819) discusses something similar
msz changed title from How to map DWI images to BIDS filenames (Aachen dataset)? to How to map DWI images to BIDS filenames 2025-05-22 15:47:41 +00:00
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q02/phantom-mri-bids#1
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