From 383372339889c55446a239411e165577973d3ff0 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Wed, 18 Dec 2024 16:14:23 -0500
Subject: [PATCH] fix: Use consistent skull-stripping pre- and post- SDC

---
 fmriprep/workflows/bold/fit.py | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
index c874b3fe..660fc024 100644
--- a/fmriprep/workflows/bold/fit.py
+++ b/fmriprep/workflows/bold/fit.py
@@ -27,7 +27,7 @@
 import nibabel as nb
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
-from niworkflows.func.util import init_enhance_and_skullstrip_bold_wf
+from niworkflows.func.util import init_enhance_and_skullstrip_bold_wf, init_skullstrip_bold_wf
 from niworkflows.interfaces.header import ValidateImage
 from niworkflows.interfaces.nitransforms import ConcatenateXFMs
 from niworkflows.interfaces.utility import KeySelect
@@ -553,7 +553,8 @@ def init_bold_fit_wf(
             )
             unwarp_wf.inputs.inputnode.metadata = layout.get_metadata(bold_file)
 
-            # fmt:off
+            skullstrip_bold_wf = init_skullstrip_bold_wf()
+
             workflow.connect([
                 (inputnode, fmap_select, [
                     ('fmap_ref', 'fmap_ref'),
@@ -578,8 +579,11 @@ def init_bold_fit_wf(
                 (unwarp_wf, ds_coreg_boldref_wf, [
                     ('outputnode.corrected', 'inputnode.boldref'),
                 ]),
-                (unwarp_wf, ds_boldmask_wf, [
-                    ('outputnode.corrected_mask', 'inputnode.boldmask'),
+                (unwarp_wf, skullstrip_bold_wf, [
+                    ('outputnode.corrected', 'inputnode.in_file'),
+                ]),
+                (skullstrip_bold_wf, ds_boldmask_wf, [
+                    ('outputnode.mask_file', 'inputnode.boldmask'),
                 ]),
                 (fmap_select, func_fit_reports_wf, [('fmap_ref', 'inputnode.fmap_ref')]),
                 (fmap_select, summary, [('sdc_method', 'distortion_correction')]),
@@ -587,10 +591,8 @@ def init_bold_fit_wf(
                     ('boldref2fmap_xfm', 'inputnode.boldref2fmap_xfm'),
                 ]),
                 (unwarp_wf, func_fit_reports_wf, [('outputnode.fieldmap', 'inputnode.fieldmap')]),
-            ])
-            # fmt:on
+            ])  # fmt:skip
         else:
-            # fmt:off
             workflow.connect([
                 (enhance_boldref_wf, ds_coreg_boldref_wf, [
                     ('outputnode.bias_corrected_file', 'inputnode.boldref'),
@@ -598,8 +600,7 @@ def init_bold_fit_wf(
                 (enhance_boldref_wf, ds_boldmask_wf, [
                     ('outputnode.mask_file', 'inputnode.boldmask'),
                 ]),
-            ])
-            # fmt:on
+            ])  # fmt:skip
     else:
         config.loggers.workflow.info('Found coregistration reference - skipping Stage 3')
         regref_buffer.inputs.boldref = precomputed['coreg_boldref']