FIX: Connect bold_mask to bold_t2s_wf

nipreps · Oct 15, 2023 · d4a84ad · d4a84ad
1 parent 4564048
commit d4a84ad
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diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
@@ -159,6 +159,7 @@ def init_bold_wf(
     workflow.connect([
         (bold_fit_wf, bold_native_wf, [
             ("outputnode.coreg_boldref", "inputnode.boldref"),
+            ("outputnode.bold_mask", "inputnode.bold_mask"),
             ("outputnode.motion_xfm", "inputnode.motion_xfm"),
             ("outputnode.boldref2fmap_xfm", "inputnode.fmapreg_xfm"),
             ("outputnode.dummy_scans", "inputnode.dummy_scans"),

diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py
@@ -692,6 +692,7 @@ def init_bold_native_wf(
         # Do NOT set motion_xfm or fieldmap_id on outputnode
         # This prevents downstream resamplers from double-dipping
         workflow.connect([
+            (inputnode, bold_t2s_wf, [("bold_mask", "inputnode.bold_mask")]),
             (boldref_bold, join_echos, [("out_file", "bold_files")]),
             (join_echos, bold_t2s_wf, [("bold_files", "inputnode.bold_file")]),
             (join_echos, outputnode, [("bold_files", "bold_echos")]),