Comments (3)
This is something we went back and forth about at our end too, but we encounter multiple subject visits more often than most I guess. I like the idea of the code being compliant to the user's wishes on this, so how about making the input DICOM directory organization dictate whether a session level will be inserted. If a session directory level is present in the DICOM directory, the BIDS source directory will also contain a session level, and the filenames will include the session key-value. Otherwise, not. I'll try to work on this next week.
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Exactly - that's my idea. If your DICOM has Session1 in there from the start, we roll with the assumption you want it in there in the BIDS, even if right now, it's just the one session. If your DICOMs live in the subject-level directory, no session gets added.
Code-wise, it doesn't look too bad to add this in.
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Added --no-sessions flag (default False) to the command line args. Avoids problems with different DICOM file sources generating different heirarchies for subjects, sessions and series (eg Horus vs Osirix vs DICOM CDs, etc). Simply add this flag to the command line and dcm2bids.py won't use sessions at all. All files within a given subjects DICOM tree will be converted as though they were one session. Let me know if this works for you - I'm others will prefer this to the forced session structure.
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Related Issues (20)
- BIDS validation error for fieldmaps after conversion HOT 16
- default readme in BIDS dataset after conversion HOT 3
- Second pass error HOT 6
- 'SerDesc' key error HOT 4
- .bval and .bvec export depends on dwi filename HOT 2
- Second pass error : KeyError: 'ScanningSequence' HOT 3
- Read-the-Docs page is an empty stub
- Not anonymizing HOT 1
- Second pass issue HOT 1
- Error when using --no-sessions option and only one subject is converted HOT 2
- Question about data structuring prior to running BIDSKIT
- Acquisition suffix is duplicated when multiple runs HOT 5
- IntendedFor fields with incorrect slash when running in Windows
- Cannot debug bidskit
- Cannot convert Tilted CT Scan
- session flag
- Files are overwritten on the second pass HOT 1
- Unable to run bidskit - "TypeError: Expected maxsize to be an integer or None" HOT 3
- Unclear specifications/ lack of examples of "Protocol_Translator.json" file
- Blip up/down for multi-echo
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