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FIX: Match mask header prior to n4 correction #443

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merged 1 commit into from
Feb 4, 2025
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FIX: Match mask header prior to n4 correction #443

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8 changes: 7 additions & 1 deletion nibabies/workflows/anatomical/surfaces.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
from niworkflows.interfaces.freesurfer import (
PatchedRobustRegister as RobustRegister,
)
from niworkflows.interfaces.header import MatchHeader
from niworkflows.interfaces.morphology import BinaryDilation
from niworkflows.interfaces.patches import FreeSurferSource
from smriprep.interfaces.freesurfer import MakeMidthickness
Expand Down Expand Up @@ -126,6 +127,9 @@
mask_dil = pe.Node(BinaryDilation(radius=3), name='mask_dil')
mask_las = pe.Node(ReorientImage(target_orientation='LAS'), name='mask_las')

# N4 has low tolerance for mismatch between input / mask
match_header = pe.Node(MatchHeader(), name='match_header')

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Added line #L131 was not covered by tests

# N4BiasCorrection occurs in MCRIBTissueSegMCRIBS (which is skipped)
# Run it (with mask to rescale intensities) prior injection
n4_mcribs = pe.Node(
Expand Down Expand Up @@ -177,7 +181,9 @@
('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
(t2w_las, n4_mcribs, [('out_file', 'input_image')]),
(mask_las, n4_mcribs, [('out_file', 'mask_image')]),
(mask_las, match_header, [('out_file', 'in_file')]),
(t2w_las, match_header, [('out_file', 'reference')]),
(match_header, n4_mcribs, [('out_file', 'mask_image')]),
(n4_mcribs, mcribs_recon, [('output_image', 't2w_file')]),
(seg_las, mcribs_recon, [('out_file', 'segmentation_file')]),
(inputnode, mcribs_postrecon, [
Expand Down