From 43e2a2550c673a3617358b825781b965359b2d9f Mon Sep 17 00:00:00 2001 From: David Meunier Date: Thu, 27 Nov 2025 12:00:53 +0100 Subject: [PATCH 1/5] stereo_padded_wmgm_mask --- macapype/pipelines/full_pipelines.py | 16 ++++++++++++++++ macapype/pipelines/rename.py | 20 ++++++++++++++++++++ 2 files changed, 36 insertions(+) diff --git a/macapype/pipelines/full_pipelines.py b/macapype/pipelines/full_pipelines.py index cddd23c83..5e4d05be2 100644 --- a/macapype/pipelines/full_pipelines.py +++ b/macapype/pipelines/full_pipelines.py @@ -618,6 +618,7 @@ def create_full_T1T2_subpipes( "stereo_wmgm_mask", "native_wmgm_mask", + "stereo_padded_wmgm_mask", "wmgm_stl", "csf_stl", @@ -1258,6 +1259,21 @@ def create_full_T1T2_subpipes( IsoSurface_brain_pipe, "outputnode.wmgm_nii", outputnode, "native_wmgm_mask", params) + if "pad_template" in params["short_preparation_pipe"].keys(): + pad_stereo_wmgm_mask = NodeParams( + ImageMath(), + params=parse_key(params["short_preparation_pipe"], + "pad_template"), + name="pad_stereo_wmgm_mask") + + seg_pipe.connect( + IsoSurface_brain_pipe, "outputnode.wmgm_nii", + pad_stereo_wmgm_mask, "op1") + + seg_pipe.connect( + pad_stereo_stereo_brain_mask, "output_image", + outputnode, "stereo_padded_wmgm_mask") + if "IsoSurface_tissues_pipe" in params: IsoSurface_tissues_pipe = create_open_IsoSurface_tissues_pipe( diff --git a/macapype/pipelines/rename.py b/macapype/pipelines/rename.py index 38cbdf618..20b409841 100644 --- a/macapype/pipelines/rename.py +++ b/macapype/pipelines/rename.py @@ -499,6 +499,26 @@ def rename_all_brain_derivatives(params, main_workflow, segment_pnh_pipe, rename_stereo_wmgm_mask, 'out_file', datasink, '@stereo_wmgm_mask') + if "pad_template" in params["short_preparation_pipe"].keys(): + + rename_stereo_padded_wmgm_mask = pe.Node( + niu.Rename(), + name="v") + v.inputs.format_string = \ + pref_deriv + "_space-stereo_desc-pad_desc-wmgm_mask" + rename_stereo_padded_wmgm_mask.inputs.parse_string = \ + parse_str + rename_stereo_padded_wmgm_mask.inputs.keep_ext = True + + main_workflow.connect( + segment_pnh_pipe, + 'outputnode.stereo_padded_segmented_brain_mask', + rename_stereo_padded_wmgm_mask, 'in_file') + + main_workflow.connect( + rename_stereo_padded_wmgm_mask, 'out_file', + datasink, '@stereo_padded_wmgm_mask') + if "IsoSurface_tissues_pipe" in params: print("Renaming csf_stl file") From b77cbbfce750277247b92c10174c301fd6af9ecf Mon Sep 17 00:00:00 2001 From: David Meunier Date: Thu, 27 Nov 2025 12:02:55 +0100 Subject: [PATCH 2/5] v --- macapype/pipelines/rename.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/macapype/pipelines/rename.py b/macapype/pipelines/rename.py index 20b409841..cc6068261 100644 --- a/macapype/pipelines/rename.py +++ b/macapype/pipelines/rename.py @@ -504,7 +504,7 @@ def rename_all_brain_derivatives(params, main_workflow, segment_pnh_pipe, rename_stereo_padded_wmgm_mask = pe.Node( niu.Rename(), name="v") - v.inputs.format_string = \ + rename_stereo_padded_wmgm_mask.inputs.format_string = \ pref_deriv + "_space-stereo_desc-pad_desc-wmgm_mask" rename_stereo_padded_wmgm_mask.inputs.parse_string = \ parse_str From 0040e67ff2a3bb4063ce9974c3b0924be61c994c Mon Sep 17 00:00:00 2001 From: David Meunier Date: Thu, 27 Nov 2025 15:44:37 +0100 Subject: [PATCH 3/5] stereo_padded_wmgm_mask --- macapype/pipelines/rename.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/macapype/pipelines/rename.py b/macapype/pipelines/rename.py index cc6068261..cad429772 100644 --- a/macapype/pipelines/rename.py +++ b/macapype/pipelines/rename.py @@ -512,7 +512,7 @@ def rename_all_brain_derivatives(params, main_workflow, segment_pnh_pipe, main_workflow.connect( segment_pnh_pipe, - 'outputnode.stereo_padded_segmented_brain_mask', + 'outputnode.stereo_padded_wmgm_mask', rename_stereo_padded_wmgm_mask, 'in_file') main_workflow.connect( From b4ca2fbe41481399640e64c44763be67179a35eb Mon Sep 17 00:00:00 2001 From: David Meunier Date: Thu, 27 Nov 2025 16:27:59 +0100 Subject: [PATCH 4/5] pad_stereo_wmgm_mask --- macapype/pipelines/full_pipelines.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/macapype/pipelines/full_pipelines.py b/macapype/pipelines/full_pipelines.py index 5e4d05be2..3d3e7fe63 100644 --- a/macapype/pipelines/full_pipelines.py +++ b/macapype/pipelines/full_pipelines.py @@ -1271,7 +1271,7 @@ def create_full_T1T2_subpipes( pad_stereo_wmgm_mask, "op1") seg_pipe.connect( - pad_stereo_stereo_brain_mask, "output_image", + pad_stereo_wmgm_mask, "output_image", outputnode, "stereo_padded_wmgm_mask") if "IsoSurface_tissues_pipe" in params: From 2d57d985fd6756776bd4ba71cc097b26bdde2be5 Mon Sep 17 00:00:00 2001 From: David Meunier Date: Fri, 12 Dec 2025 10:16:05 +0100 Subject: [PATCH 5/5] flake8 --- macapype/pipelines/full_pipelines.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/macapype/pipelines/full_pipelines.py b/macapype/pipelines/full_pipelines.py index 3d3e7fe63..f49463fd6 100644 --- a/macapype/pipelines/full_pipelines.py +++ b/macapype/pipelines/full_pipelines.py @@ -1262,8 +1262,8 @@ def create_full_T1T2_subpipes( if "pad_template" in params["short_preparation_pipe"].keys(): pad_stereo_wmgm_mask = NodeParams( ImageMath(), - params=parse_key(params["short_preparation_pipe"], - "pad_template"), + params=parse_key( + params["short_preparation_pipe"], "pad_template"), name="pad_stereo_wmgm_mask") seg_pipe.connect(