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Add padded wmgm #316

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Merged
davidmeunier79 merged 5 commits into from
Dec 15, 2025
Merged

Add padded wmgm #316

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43e2a25
stereo_padded_wmgm_mask
davidmeunier79 Nov 27, 2025
b77cbbf
v
davidmeunier79 Nov 27, 2025
0040e67
stereo_padded_wmgm_mask
davidmeunier79 Nov 27, 2025
b4ca2fb
pad_stereo_wmgm_mask
davidmeunier79 Nov 27, 2025
2d57d98
flake8
davidmeunier79 Dec 12, 2025
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16 changes: 16 additions & 0 deletions macapype/pipelines/full_pipelines.py
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Original file line number Diff line number Diff line change
Expand Up @@ -618,6 +618,7 @@ def create_full_T1T2_subpipes(

"stereo_wmgm_mask",
"native_wmgm_mask",
"stereo_padded_wmgm_mask",
"wmgm_stl",

"csf_stl",
Expand Down Expand Up @@ -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_wmgm_mask, "output_image",
outputnode, "stereo_padded_wmgm_mask")

if "IsoSurface_tissues_pipe" in params:

IsoSurface_tissues_pipe = create_open_IsoSurface_tissues_pipe(
Expand Down
20 changes: 20 additions & 0 deletions macapype/pipelines/rename.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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")
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
rename_stereo_padded_wmgm_mask.inputs.keep_ext = True

main_workflow.connect(
segment_pnh_pipe,
'outputnode.stereo_padded_wmgm_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")
Expand Down