From 74ba3113325848932992ecc79420b1edc6a409dd Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Sat, 1 Mar 2025 15:19:05 -0500 Subject: [PATCH] fix(brain_extraction_wf): Pass inu_n4 to atropos_wf antsBrainExtraction.sh passes the original N4 corrected image to Atropos, where we have been running a masked N4 before Atropos. We have examples where this difference leads to failures that do not occur in the original ANTs workflow. Further, if we do run Atropos, then this result is discarded and N4 is run using a white-matter mask. This patch therefore simply passes the original N4 image to the Atropos workflow, but otherwise leaves the workflow unchanged. --- niworkflows/anat/ants.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/niworkflows/anat/ants.py b/niworkflows/anat/ants.py index 17630d710b9..a077d91295d 100644 --- a/niworkflows/anat/ants.py +++ b/niworkflows/anat/ants.py @@ -459,7 +459,7 @@ def init_brain_extraction_wf( ]) wf.connect([ (inputnode, atropos_wf, [("in_files", "inputnode.in_files")]), - (inu_n4_final, atropos_wf, [("output_image", "inputnode.in_corrected")]), + (inu_n4, atropos_wf, [("output_image", "inputnode.in_corrected")]), (thr_brainmask, atropos_wf, [("output_image", "inputnode.in_mask")]), (atropos_wf, outputnode, [ ("outputnode.out_file", "out_file"),