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Fixes for --register-to-mri workflow#94

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akhanf merged 8 commits intomainfrom
djay/fix-bugs
Feb 15, 2026
Merged

Fixes for --register-to-mri workflow#94
akhanf merged 8 commits intomainfrom
djay/fix-bugs

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@Dhananjhay
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This PR fixes the following:

  1. Use of consistent suffix (only using nii.gz now)
  2. Use Snakebids expand function to input correct values of wildcards
  3. Remove hardcoded inputs to wildcards values

Comment thread spimquant/workflow/rules/preproc_mri.smk Outdated
@akhanf
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akhanf commented Feb 6, 2026

Thanks! - left one comment to address, and will need to run the quality_fix task

@Dhananjhay Dhananjhay requested a review from akhanf February 9, 2026 16:50
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akhanf commented Feb 12, 2026

changes look good to me, but I'll give it a wet-run test while I am at it..

expand without filtering on wildcards was causing all subjects T2w images
to be returnEd, selecting first, so always first subject.
no test case yet but was used to test functionality
@akhanf akhanf changed the title Patch to ensure consistency across codebase Fixes for --register-to-mri workflow Feb 15, 2026
@akhanf akhanf merged commit ee53cd8 into main Feb 15, 2026
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@akhanf akhanf deleted the djay/fix-bugs branch February 15, 2026 20:23
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2 participants