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REL: 25.2.7 - #3695
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effigies wants to merge 4 commits into
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REL: 25.2.7#3695effigies wants to merge 4 commits into
effigies wants to merge 4 commits into
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This is a small pull request to give time for some feedback on an upcoming release on the 25.2.x LTS series.
This branch can be tested from
docker://nipreps/fmriprep:25.2.7-rc1This has a change to one workflow step that has the potential to impact every dataset: nipreps/niworkflows#1064
The idea is that we have an average bold reference image resampled to MNI. We perform a simple affine registration so we can project the MNI brain mask onto our BOLD and run N4 bias field correction only within the mask. The registration happens in two stages, both affine (12-dof), with the first allowed to make larger moves while the second is refined. The problem we found in nipreps/niworkflows#1000 is that the initial affine could sometimes add large shear or scale components, resulting in a highly skewed mask that the second stage could not correct. The fix is to change the first step to rigid (6-dof), to avoid this edge case. The second affine step still has the additional degrees of freedom to account for differences in brain shape.
The mask that is generated is thrown away after this use; the only impact this has is on what voxels are in-scope to fit a bias field estimate.
cc @claraElk @HippocampusGirl Does this seem safe enough to you, or would you like to run your tests to confirm?