From 4ff1f40ff14192f4794183f5089751ef6f0a318b Mon Sep 17 00:00:00 2001 From: David Meunier Date: Fri, 29 Mar 2024 16:57:43 +0100 Subject: [PATCH] stereo_brain_mask --- macapype/pipelines/full_pipelines.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/macapype/pipelines/full_pipelines.py b/macapype/pipelines/full_pipelines.py index 0a94198a..fb0750cf 100644 --- a/macapype/pipelines/full_pipelines.py +++ b/macapype/pipelines/full_pipelines.py @@ -232,7 +232,6 @@ def create_full_spm_subpipes( else: print("Using native external mask {}".format(mask_file)) - outputnode.inputs.native_brain_mask = mask_file # apply transfo to list apply_crop_external_mask = pe.Node(RegResample(inter_val="NN"), @@ -251,8 +250,13 @@ def create_full_spm_subpipes( debias, "b") # outputnode - seg_pipe.connect(debias, "debiased_mask_file", - outputnode, "stereo_brain_mask") + + if mask_file is None: + seg_pipe.connect(debias, "debiased_mask_file", + outputnode, "stereo_brain_mask") + else: + seg_pipe.connect(apply_crop_external_mask, "out_file", + outputnode, "stereo_brain_mask") seg_pipe.connect(debias, 't1_debiased_brain_file', outputnode, "stereo_masked_debiased_T1") @@ -272,6 +276,8 @@ def create_full_spm_subpipes( seg_pipe, data_preparation_pipe, inputnode, debias, "debiased_mask_file", outputnode, "native_brain_mask", params) + else: + outputnode.inputs.native_brain_mask = mask_file pad_back( seg_pipe, data_preparation_pipe, inputnode,