Mesh spm

.github/workflows/build_on_prerelease.yml

@@ -73,7 +73,7 @@ jobs:
 
     strategy:
         matrix:
-            soft: [ANTS, ANTS_T1]
+            soft: [ANTS, ANTS_T1, SPM_native]
     steps:
       - name: Pull latest docker image
         run:

.github/workflows/build_on_release.yml

@@ -72,7 +72,7 @@ jobs:
 
     strategy:
         matrix:
-            soft: [ANTS, ANTS_T1]
+            soft: [ANTS, ANTS_T1, SPM_native]
     steps:
       - name: Pull latest docker image
         run:

macapype/pipelines/full_pipelines.py

@@ -129,6 +129,7 @@ def create_full_spm_subpipes(
     outputnode = pe.Node(
         niu.IdentityInterface(fields=['brain_mask', 'segmented_brain_mask',
                                       'debiased_T1', 'debiased_brain',
+                                      "wmgm_stl",
                                       'prob_wm', 'prob_gm', 'prob_csf']),
         name='outputnode')
     # preprocessing
@@ -673,6 +674,8 @@ def create_full_spm_subpipes(
         seg_pipe.connect(inputnode, 'indiv_params',
                          mask_from_seg_pipe, 'inputnode.indiv_params')
 
+        seg_pipe.connect(mask_from_seg_pipe, "wmgm2mesh.stl_file",
+                         outputnode, 'wmgm_stl')
         # seg_mask
         if pad and space == "native":
             if "short_preparation_pipe" in params.keys():

macapype/pipelines/rename.py

@@ -458,3 +458,20 @@ def rename_all_derivatives(params, main_workflow, segment_pnh_pipe,
         main_workflow.connect(
             rename_segmented_brain_mask, 'out_file',
             datasink, '@segmented_brain_mask')
+
+        print("Renaming wmgm_stl file")
+
+        rename_wmgm_stl = pe.Node(niu.Rename(),
+                                  name="rename_wmgm_stl")
+        rename_wmgm_stl.inputs.format_string = \
+            pref_deriv + "_space-{}_desc-wmgm_mask".format(space)
+        rename_wmgm_stl.inputs.parse_string = parse_str
+        rename_wmgm_stl.inputs.keep_ext = True
+
+        main_workflow.connect(
+            segment_pnh_pipe, 'outputnode.wmgm_stl',
+            rename_wmgm_stl, 'in_file')
+
+        main_workflow.connect(
+            rename_wmgm_stl, 'out_file',
+            datasink, '@wmgm_stl')

macapype/pipelines/segment.py

@@ -5,10 +5,13 @@
 
 import nipype.interfaces.spm as spm
 
-from ..nodes.segment import (AtroposN4, merge_masks,
+from ..nodes.segment import (AtroposN4, merge_masks, BinaryFillHoles,
                              merge_imgs, split_indexed_mask, copy_header,
                              compute_5tt, fill_list_vol)
 
+
+from macapype.nodes.surface import wrap_afni_IsoSurface
+
 from ..utils.misc import (gunzip, merge_3_elem_to_list,
                           get_pattern, get_list_length, get_index)
 
@@ -845,7 +848,6 @@ def create_native_old_segment_pipe(params_template, params={},
 ###############################################################################
 # create mask from segment
 def create_mask_from_seg_pipe(params={}, name="mask_from_seg_pipe"):
-
     """
     Description:  mask from segmentation tissues
 
@@ -916,4 +918,55 @@ def create_mask_from_seg_pipe(params={}, name="mask_from_seg_pipe"):
     seg_pipe.connect(bin_csf, 'out_file',
                      merge_indexed_mask, "mask_csf_file")
 
+    # Compute union of the 3 tissues
+    # Done with 2 fslmaths as it seems to hard to do it
+    wmgm_union = pe.Node(fsl.BinaryMaths(), name="wmgm_union")
+    wmgm_union.inputs.operation = "add"
+    seg_pipe.connect(bin_gm, 'out_file', wmgm_union, 'in_file')
+    seg_pipe.connect(bin_wm, 'out_file', wmgm_union, 'operand_file')
+
+    tissues_union = pe.Node(fsl.BinaryMaths(), name="tissues_union")
+    tissues_union.inputs.operation = "add"
+    seg_pipe.connect(wmgm_union, 'out_file', tissues_union, 'in_file')
+    seg_pipe.connect(bin_csf, 'out_file',
+                     tissues_union, 'operand_file')
+
+    # Opening (dilating) mask
+    dilate_mask = NodeParams(fsl.DilateImage(),
+                             params=parse_key(params, "dilate_mask"),
+                             name="dilate_mask")
+
+    dilate_mask.inputs.operation = "mean"  # Arbitrary operation
+    seg_pipe.connect(tissues_union, 'out_file', dilate_mask, 'in_file')
+
+    # fill holes of dilate_mask
+    fill_holes_dil = pe.Node(BinaryFillHoles(), name="fill_holes_dil")
+    seg_pipe.connect(dilate_mask, 'out_file', fill_holes_dil, 'in_file')
+
+    # Eroding mask
+    erode_mask = NodeParams(fsl.ErodeImage(),
+                            params=parse_key(params, "erode_mask"),
+                            name="erode_mask")
+
+    seg_pipe.connect(tissues_union, 'out_file', erode_mask, 'in_file')
+
+    # fill holes of erode_mask
+    fill_holes = pe.Node(BinaryFillHoles(), name="fill_holes")
+    seg_pipe.connect(erode_mask, 'out_file', fill_holes, 'in_file')
+
+    # bin mask
+    bin_mask = pe.Node(interface=fsl.UnaryMaths(), name="bin_mask")
+    bin_mask.inputs.operation = "bin"
+
+    seg_pipe.connect(fill_holes, 'out_file', bin_mask, 'in_file')
+
+    # wmgm2mesh
+    wmgm2mesh = pe.Node(
+        interface=niu.Function(input_names=["nii_file"],
+                               output_names=["stl_file"],
+                               function=wrap_afni_IsoSurface),
+        name="wmgm2mesh")
+
+    seg_pipe.connect(bin_mask, 'out_file', wmgm2mesh, "nii_file")
+
     return seg_pipe