update_bids_layout.py misses DWI .bval/.bvec renaming and IntendedFor in DWI json file #7

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opened 2026-07-03 16:53:19 +00:00 by ron · 1 comment

ron commented

2026-07-03 16:53:19 +00:00

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While using update_bids_layout.py to update the Mannheim and Heidelberg Q01 BIDS datasets, I noticed two issues with the DWI updates:

1. The script renames the DWI NIfTI and JSON files (e.g. adding dir-PA), but does not rename the corresponding .bval and .bvec files. As a temporary workaround, I implemented a small script (rename_dwi_bval_bvec.py) to rename them
2. The reverse PE EPI JSONs moved to fmap/ do not receive an IntendedFor entry pointing to the corresponding DWI image. I therefore had to add this manually using add_dwi_intendedfor.py

I compared this with the original fix_dwi_sdc.sh script, which correctly handled both the .bval/.bvec renaming and the IntendedFor update. It looks like these two steps may have been omitted during the Python port.

Adding these two updates would make the resulting dataset fully BIDS compliant and remove the need for manual post processing.

While using update_bids_layout.py to update the Mannheim and Heidelberg Q01 BIDS datasets, I noticed two issues with the DWI updates: 1. The script renames the DWI NIfTI and JSON files (e.g. adding dir-PA), but does not rename the corresponding .bval and .bvec files. As a temporary workaround, I implemented a small script (rename_dwi_bval_bvec.py) to rename them 2. The reverse PE EPI JSONs moved to fmap/ do not receive an IntendedFor entry pointing to the corresponding DWI image. I therefore had to add this manually using add_dwi_intendedfor.py I compared this with the original fix_dwi_sdc.sh script, which correctly handled both the .bval/.bvec renaming and the IntendedFor update. It looks like these two steps may have been omitted during the Python port. Adding these two updates would make the resulting dataset fully BIDS compliant and remove the need for manual post processing.

rename_dwi_bval_bvec.py.txt

912 B

add_dwi_intendedfor.py.txt

1.2 KiB

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