q02/phantom-mri-bids
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How to determine subject name for BIDS #2

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opened 2025-05-06 18:38:58 +00:00 by msz · 1 comment
msz commented 2025-05-06 18:38:58 +00:00
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Heudiconv needs the subject ID to generate the right file / folder names for BIDS. It can take it from several sources:

  • explicitly given on the command line (that's what I currently used for Aachen)
  • taken from the folder name
  • taken from the DICOM headers
  • any of the above, but anonymized with an external command (--anon-cmd).

Looking at the DICOMs with phantom scans from:

it seems that we cannot apply the same method to all sites. These are the values from the DICOM headers:

Aachen Heidelberg Mannheim
(0010,0010) PatientName P250120 Test^Test TRR379_Q01_phantom
(0010,0020) PatientID P250120 24.12.03-11:36:05-STD-1.3.12.2.1107.5.2.43.167086 TRR379_Q01_phantom

What would be the preferred method to generate IDs in the workflow?

Heudiconv needs the subject ID to generate the right file / folder names for BIDS. It can take it from several sources: - explicitly given on the command line (that's what I currently used for Aachen) - taken from the folder name - taken from the DICOM headers - any of the above, but anonymized with an external command (`--anon-cmd`). Looking at the DICOMs with phantom scans from: - https://hub.trr379.de/q01/phantom-mri-dicom-aachen - https://hub.trr379.de/q01/phantom-mri-dicom-heidelberg - https://hub.trr379.de/q01/phantom-mri-dicom-mannheim it seems that we cannot apply the same method to all sites. These are the values from the DICOM headers: | | Aachen | Heidelberg | Mannheim | |---------|---------|---------|---------| | (0010,0010) PatientName | P250120 | Test^Test | TRR379_Q01_phantom | | (0010,0020) PatientID | P250120 | 24.12.03-11:36:05-STD-1.3.12.2.1107.5.2.43.167086 | TRR379_Q01_phantom | What would be the preferred method to generate IDs in the workflow?
mih commented 2025-05-07 17:08:08 +00:00
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For the phantom dataset it is sufficient to take a subject name as an explicit argument. For the actual data, the solution will likely differ per site, because all site have full freedom to encode the subject identifiers any way they see fit.

How individual site BIDS datasets are integrated into a joint dataset is an open question with two parts:

  • will it be done?
  • and if so, how?

Integrating into a joint dataset depends on whether the underlying data can be made programatically accessible at all sites.

For the phantom dataset it is sufficient to take a subject name as an explicit argument. For the actual data, the solution will likely differ per site, because all site have full freedom to encode the subject identifiers any way they see fit. How individual site BIDS datasets are integrated into a joint dataset is an open question with two parts: - will it be done? - and if so, how? Integrating into a joint dataset depends on whether the underlying data can be made programatically accessible at all sites.
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q02/phantom-mri-bids#2
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