Add padded wmgm (#316)

* stereo_padded_wmgm_mask

Author: davidmeunier79

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_wmgm_mask, "output_image",
+                outputnode, "stereo_padded_wmgm_mask")
+
     if "IsoSurface_tissues_pipe" in params:
 
         IsoSurface_tissues_pipe = create_open_IsoSurface_tissues_pipe(

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")
+            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")