Comments (8)
You're also correct that sessions are optional in the BIDS specification. bidskit assumes sessions by default, but can run without session handling using the --no-sessions flag.
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Bidskit should be able to handle "-" and "_" following the resolution of Issue #61. Let me check what's happening with the docker container (I'm assuming you're using Docker to run bidskit based on your other comments). One possible workaround (I haven't tested this) would be to place all the series directories (fieldmap_BOLD_1, etc) within a dummy session directory called "1". The underscore check only applies to the subject and session names, not the series names. The final subject data structure would then be sub-027/ses-1/... and filenames would include "ses-1".
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I was not able to get the Docker version to work at all -- the above is using the pip install version.
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Oh - I am not using sessions. I was under the impression that sessions are optional.
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The pip version is still at 1.2.3. Will try to get that updated today. Are you able to install bidskit using setup.py in your environment?
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Yeah. It's just the Docker version that fails.
from bidskit.
The PyPi version has been updated to 2019.8.16 - let me know if that works out of the box. I'll be looking at the Docker issues today.
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Ok, apparently --no-sessions
is all I needed for this one.
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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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