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FIX: Pass sbref files to SyN workflow #3060

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merged 3 commits into from
Jul 31, 2023

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effigies
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Changes proposed in this pull request

The improvements to SDC to detect sbref files and prefer them needed to come with passing sbrefs to the SyN workflow.

Fixes #3046.

Documentation that should be reviewed

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codecov bot commented Jul 14, 2023

Codecov Report

Patch coverage has no change and project coverage change: -0.07% ⚠️

Comparison is base (b5619db) 49.43% compared to head (b574f62) 49.36%.

❗ Current head b574f62 differs from pull request most recent head e09c7b5. Consider uploading reports for the commit e09c7b5 to get more accurate results

Additional details and impacted files
@@               Coverage Diff                @@
##           maint/23.1.x    #3060      +/-   ##
================================================
- Coverage         49.43%   49.36%   -0.07%     
================================================
  Files                46       46              
  Lines              3599     3604       +5     
================================================
  Hits               1779     1779              
- Misses             1820     1825       +5     
Files Changed Coverage Δ
fmriprep/workflows/base.py 10.00% <0.00%> (-0.26%) ⬇️
fmriprep/workflows/bold/base.py 20.47% <0.00%> (-0.09%) ⬇️

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@effigies
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@mgxd If you have an opportunity to review this, I would appreciate it. I've tested it with the dataset submitted in #3046, so it works, just needs code review.

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This seems fine, but feels dirty accessing a "private" attribute - I've opened up nipreps/sdcflows#383

fmriprep/workflows/base.py Outdated Show resolved Hide resolved
@effigies
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This seems fine, but feels dirty accessing a "private" attribute

I would like to get away from this structure entirely in 23.2.x by passing around a dict of workflows (or at least outputnode/buffernodes), but I needed to squeeze this in as a minimal bug-fix and couldn't see another way without replicating the logic.

@mgxd mgxd merged commit fdfb699 into nipreps:maint/23.1.x Jul 31, 2023
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@effigies effigies deleted the fix/sbref-syn branch July 31, 2023 16:07
effigies added a commit that referenced this pull request Aug 1, 2023
23.1.4 (August 1, 2023)

Patch release in the 23.1.x series.

This release prioritizes single-band reference BOLD images during SyN-SDC schemes.
Additionally, an indices inconsistency was fixed for CIFTI volumetric data.

* FIX: Pass sbref files to SyN workflow (#3060)
* FIX: Generate CIFTI volume structure indices in column-major order (nipreps/niworkflows#815)
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2 participants