Fix spm native

.github/workflows/build_on_prerelease.yml

@@ -102,15 +102,15 @@ jobs:
 
       - name: Running test pipeline macaque_prime-de
         run: |
-            docker run -i -v /home/ubuntu/actions-runner/_work/macapype/macapype/${{ matrix.soft }}/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de/ -out /data/macaque_prime-de/results -soft ${{ matrix.soft }}_prep -species macaque -sub 032140 -ses 001 -deriv -pad
+            docker run -i -v /home/ubuntu/actions-runner/_work/macapype/macapype/${{ matrix.soft }}/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/macaque_prime-de/ -out /data/macaque_prime-de/results -soft ${{ matrix.soft }} -species macaque -sub 032140 -ses 001 -deriv -pad
 
       - name: Running test pipeline marmo-marmobrain
         run: |
-            docker run -i -v /home/ubuntu/actions-runner/_work/macapype/macapype/${{ matrix.soft }}/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft ${{ matrix.soft }}_prep -species marmo -sub Percy -ses 01 -deriv -pad
+            docker run -i -v /home/ubuntu/actions-runner/_work/macapype/macapype/${{ matrix.soft }}/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/marmo-marmobrain -out /data/marmo-marmobrain/results -soft ${{ matrix.soft }} -species marmo -sub Percy -ses 01 -deriv -pad
 
       - name: Running test pipeline baboon-cerimed-adrien
         run: |
-            docker run -i -v /home/ubuntu/actions-runner/_work/macapype/macapype/${{ matrix.soft }}/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/baboon-cerimed-adrien -out /data/baboon-cerimed-adrien/results -soft ${{ matrix.soft }}_prep -species baboon -sub Fidji -ses 01 -deriv -pad
+            docker run -i -v /home/ubuntu/actions-runner/_work/macapype/macapype/${{ matrix.soft }}/macapype_CI:/data macatools/macapype:latest segment_pnh -data /data/baboon-cerimed-adrien -out /data/baboon-cerimed-adrien/results -soft ${{ matrix.soft }} -species baboon -sub Fidji -ses 01 -deriv -pad
 
       - name: Cleaning dataset
         run:

macapype/nodes/surface.py

@@ -119,26 +119,6 @@ def wrap_nii2mesh(nii_file):
     assert ret == 0, "Error, cmd {} did not work".format(cmd)
     return stl_file
 
-def wrap_afni_IsoSurface (nii_file):
-
-    import os
-    from nipype.utils.filemanip import split_filename as split_f
-
-    path, fname, ext = split_f(nii_file)
-
-    stl_file = os.path.abspath(fname + ".stl")
-
-    isoval=1
-    cmd = "IsoSurface -isoval {} -input {} -Tsmooth 0.1 100  -remesh 0.5 -overwrite -autocrop -o {}".format(
-        isoval, nii_file, stl_file)
-
-    ret = os.system(cmd)
-
-    print(ret)
-
-    assert ret == 0, "Error, cmd {} did not work".format(cmd)
-    return stl_file
-
 
 # ### wrapping afni IsoSurface
 def wrap_afni_IsoSurface(nii_file):

macapype/pipelines/full_pipelines.py

@@ -40,7 +40,7 @@
                             create_extract_T1_pipe)
 
 from .surface import (create_nii_to_mesh_pipe, create_nii_to_mesh_fs_pipe,
-                      create_nii2mesh_brain_pipe)
+                      create_nii2mesh_brain_pipe, create_IsoSurface_brain_pipe)
 
 from macapype.utils.misc import parse_key, list_input_files, show_files
 
@@ -2628,6 +2628,38 @@ def create_full_ants_subpipes(
 
         seg_pipe.connect(nii2mesh_brain_pipe, "outputnode.wmgm_nii",
                          outputnode, 'wmgm_mask')
+    elif "IsoSurface_brain_pipe" in params.keys():
+
+        IsoSurface_brain_pipe = create_IsoSurface_brain_pipe(
+            params=parse_key(params["brain_segment_pipe"],
+                             "IsoSurface_brain_pipe"))
+
+        if pad:
+            if "native_to_stereo_pipe" in params.keys():
+
+                seg_pipe.connect(apply_stereo_seg_mask, "out_file",
+                                 IsoSurface_brain_pipe,
+                                 'inputnode.segmented_file')
+
+                seg_pipe.connect(IsoSurface_brain_pipe, "outputnode.wmgm_stl",
+                                 outputnode, 'stereo_wmgm_stl')
+
+                seg_pipe.connect(IsoSurface_brain_pipe, "outputnode.wmgm_nii",
+                                 outputnode, 'stereo_wmgm_mask')
+
+            elif space == "native":
+                seg_pipe.connect(pad_seg_mask, "out_file",
+                                 IsoSurface_brain_pipe,
+                                 'inputnode.segmented_file')
+        else:
+            seg_pipe.connect(brain_segment_pipe, "outputnode.segmented_file",
+                             IsoSurface_brain_pipe, 'inputnode.segmented_file')
+
+        seg_pipe.connect(IsoSurface_brain_pipe, "outputnode.wmgm_stl",
+                         outputnode, 'wmgm_stl')
+
+        seg_pipe.connect(IsoSurface_brain_pipe, "outputnode.wmgm_nii",
+                         outputnode, 'wmgm_mask')
 
     elif 'nii_to_mesh_pipe' in params.keys():
         # kept for compatibility but nii2mesh is prefered...
@@ -3811,4 +3843,37 @@ def create_full_T1_ants_subpipes(params_template, params_template_aladin,
         seg_pipe.connect(nii2mesh_brain_pipe, "outputnode.wmgm_nii",
                          outputnode, 'wmgm_mask')
 
+    elif "IsoSurface_brain_pipe" in params["brain_segment_pipe"]:
+
+        IsoSurface_brain_pipe = create_IsoSurface_brain_pipe(
+            params=parse_key(params["brain_segment_pipe"],
+                             "IsoSurface_brain_pipe"))
+
+        if pad:
+            if "native_to_stereo_pipe" in params.keys():
+
+                seg_pipe.connect(apply_stereo_seg_mask, "out_file",
+                                 IsoSurface_brain_pipe,
+                                 'inputnode.segmented_file')
+
+                seg_pipe.connect(IsoSurface_brain_pipe, "outputnode.wmgm_stl",
+                                 outputnode, 'stereo_wmgm_stl')
+
+                seg_pipe.connect(IsoSurface_brain_pipe, "outputnode.wmgm_nii",
+                                 outputnode, 'stereo_wmgm_mask')
+
+            elif space == "native":
+                seg_pipe.connect(pad_seg_mask, "out_file",
+                                 IsoSurface_brain_pipe,
+                                 'inputnode.segmented_file')
+        else:
+            seg_pipe.connect(brain_segment_pipe, "outputnode.segmented_file",
+                             IsoSurface_brain_pipe, 'inputnode.segmented_file')
+
+        seg_pipe.connect(IsoSurface_brain_pipe, "outputnode.wmgm_stl",
+                         outputnode, 'wmgm_stl')
+
+        seg_pipe.connect(IsoSurface_brain_pipe, "outputnode.wmgm_nii",
+                         outputnode, 'wmgm_mask')
+
     return seg_pipe

macapype/pipelines/segment.py

@@ -5,7 +5,7 @@
 
 import nipype.interfaces.spm as spm
 
-from ..nodes.segment import (AtroposN4, BinaryFillHoles, merge_masks,
+from ..nodes.segment import (AtroposN4, merge_masks,
                              merge_imgs, split_indexed_mask, copy_header,
                              compute_5tt, fill_list_vol)
 
@@ -724,31 +724,12 @@ def create_native_old_segment_pipe(params_template, params={},
     assert set_spm(), \
         "Error, SPM was not found, cannot run SPM old segment pipeline"
 
-    unzip = pe.Node(
-        interface=niu.Function(input_names=['zipped_file'],
-                               output_names=["unzipped_file"],
-                               function=gunzip),
-        name="unzip")
-
-    seg_pipe.connect(inputnode, 'T1', unzip, 'zipped_file')
-
-    # Segment in to 6 tissues
-    segment = NodeParams(spm.Segment(),
-                         params=parse_key(params, "segment"),
-                         name="old_segment")
-
-    segment.inputs.tissue_prob_maps = [params_template["template_gm"],
-                                       params_template["template_wm"],
-                                       params_template["template_csf"]]
-
-    seg_pipe.connect(unzip, 'unzipped_file', segment, 'data')
-
     # gm
     register_gm_to_nat = pe.Node(fsl.ApplyXFM(), name="register_gm_to_nat")
-    register_gm_to_nat.inputs.output_type = "NIFTI_GZ"  # for SPM segment
+    register_gm_to_nat.inputs.output_type = "NIFTI"  # for SPM segment
+    register_gm_to_nat.inputs.interp = "nearestneighbour"
 
-    seg_pipe.connect(segment, 'native_gm_image',
-                     register_gm_to_nat, 'in_file')
+    register_gm_to_nat.inputs.in_file = params_template["template_gm"]
 
     seg_pipe.connect(inputnode, 'native_T1',
                      register_gm_to_nat, 'reference')
@@ -758,10 +739,10 @@ def create_native_old_segment_pipe(params_template, params={},
 
     # wm
     register_wm_to_nat = pe.Node(fsl.ApplyXFM(), name="register_wm_to_nat")
-    register_wm_to_nat.inputs.output_type = "NIFTI_GZ"  # for SPM segment
+    register_wm_to_nat.inputs.output_type = "NIFTI"  # for SPM segment
+    register_wm_to_nat.inputs.interp = "nearestneighbour"
 
-    seg_pipe.connect(segment, 'native_wm_image',
-                     register_wm_to_nat, 'in_file')
+    register_wm_to_nat.inputs.in_file = params_template["template_wm"]
 
     seg_pipe.connect(inputnode, 'native_T1',
                      register_wm_to_nat, 'reference')
@@ -771,23 +752,51 @@ def create_native_old_segment_pipe(params_template, params={},
 
     # csf
     register_csf_to_nat = pe.Node(fsl.ApplyXFM(), name="register_csf_to_nat")
-    register_csf_to_nat.inputs.output_type = "NIFTI_GZ"  # for SPM segment
+    register_csf_to_nat.inputs.output_type = "NIFTI"  # for SPM segment
+    register_csf_to_nat.inputs.interp = "nearestneighbour"
 
-    seg_pipe.connect(segment, 'native_csf_image',
-                     register_csf_to_nat, 'in_file')
+    register_csf_to_nat.inputs.in_file = params_template["template_csf"]
 
     seg_pipe.connect(inputnode, 'native_T1',
                      register_csf_to_nat, 'reference')
 
     seg_pipe.connect(inputnode, 'inv_transfo_file',
                      register_csf_to_nat, "in_matrix_file")
+    # unzip T1
+    unzip = pe.Node(
+        interface=niu.Function(input_names=['zipped_file'],
+                               output_names=["unzipped_file"],
+                               function=gunzip),
+        name="unzip")
+
+    seg_pipe.connect(inputnode, 'T1', unzip, 'zipped_file')
+
+    # merge_tissue_files
+    merge_tissue_files = pe.Node(
+        interface=niu.Merge(3),
+        name="merge_tissue_files")
+
+    seg_pipe.connect(register_gm_to_nat, "out_file", merge_tissue_files, 'in1')
+    seg_pipe.connect(register_wm_to_nat, "out_file", merge_tissue_files, 'in2')
+    seg_pipe.connect(register_csf_to_nat, "out_file",
+                     merge_tissue_files, 'in3')
+
+    # Segment in to 6 tissues
+    segment = NodeParams(spm.Segment(),
+                         params=parse_key(params, "segment"),
+                         name="old_segment")
+
+    seg_pipe.connect(merge_tissue_files, "out",
+                     segment, "tissue_prob_maps")
+
+    seg_pipe.connect(unzip, 'unzipped_file', segment, 'data')
 
     # threshold_gm
     threshold_gm = NodeParams(fsl.Threshold(),
                               params=parse_key(params, "threshold_gm"),
                               name="threshold_gm")
 
-    seg_pipe.connect(register_gm_to_nat, 'out_file', threshold_gm, 'in_file')
+    seg_pipe.connect(segment, 'native_gm_image', threshold_gm, 'in_file')
 
     seg_pipe.connect(
         inputnode, ('indiv_params', parse_key, "threshold_gm"),
@@ -798,7 +807,7 @@ def create_native_old_segment_pipe(params_template, params={},
                               params=parse_key(params, "threshold_wm"),
                               name="threshold_wm")
 
-    seg_pipe.connect(register_wm_to_nat, 'out_file', threshold_wm, 'in_file')
+    seg_pipe.connect(segment, 'native_wm_image', threshold_wm, 'in_file')
 
     seg_pipe.connect(
         inputnode, ('indiv_params', parse_key, "threshold_wm"),
@@ -809,7 +818,7 @@ def create_native_old_segment_pipe(params_template, params={},
                                params=parse_key(params, "threshold_csf"),
                                name="threshold_csf")
 
-    seg_pipe.connect(register_csf_to_nat, 'out_file', threshold_csf, 'in_file')
+    seg_pipe.connect(segment, 'native_csf_image', threshold_csf, 'in_file')
 
     seg_pipe.connect(
         inputnode, ('indiv_params', parse_key, "threshold_csf"),
@@ -826,9 +835,9 @@ def create_native_old_segment_pipe(params_template, params={},
     seg_pipe.connect(threshold_wm, 'out_file', outputnode, 'threshold_wm')
     seg_pipe.connect(threshold_csf, 'out_file', outputnode, 'threshold_csf')
 
-    seg_pipe.connect(register_gm_to_nat, 'out_file', outputnode, 'prob_gm')
-    seg_pipe.connect(register_wm_to_nat, 'out_file', outputnode, 'prob_wm')
-    seg_pipe.connect(register_csf_to_nat, 'out_file', outputnode, 'prob_csf')
+    seg_pipe.connect(segment, 'native_gm_image', outputnode, 'prob_gm')
+    seg_pipe.connect(segment, 'native_wm_image', outputnode, 'prob_wm')
+    seg_pipe.connect(segment, 'native_csf_image', outputnode, 'prob_csf')
 
     return seg_pipe
 
@@ -892,42 +901,6 @@ def create_mask_from_seg_pipe(params={}, name="mask_from_seg_pipe"):
     seg_pipe.connect(inputnode, 'mask_wm',
                                 bin_wm, 'in_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')
-
     # merge to index
     merge_indexed_mask = NodeParams(
         interface=niu.Function(input_names=["mask_csf_file", "mask_wm_file",

macapype/pipelines/surface.py

@@ -9,7 +9,8 @@
 import macapype.nodes.register as reg
 
 from macapype.nodes.surface import (Meshify, split_LR_mask,
-                                    wrap_nii2mesh, merge_tissues)
+                                    wrap_nii2mesh,
+                                    wrap_afni_IsoSurface, merge_tissues)
 
 from macapype.utils.utils_nodes import parse_key, NodeParams
 
@@ -683,3 +684,55 @@ def create_nii2mesh_brain_pipe(params={},
     nii2mesh_brain_pipe.connect(wmgm2mesh, 'stl_file', outputnode, "wmgm_stl")
 
     return nii2mesh_brain_pipe
+
+
+def create_IsoSurface_brain_pipe(params={},
+                                 name="IsoSurface_brain_pipe"):
+
+    # creating pipeline
+    IsoSurface_brain_pipe = pe.Workflow(name=name)
+
+    # creating inputnode
+    inputnode = pe.Node(
+        niu.IdentityInterface(
+            fields=["segmented_file"]),
+        name='inputnode')
+
+    # merge_brain_tissues
+    merge_brain_tissues = NodeParams(
+        interface=niu.Function(input_names=["dseg_file", "keep_indexes"],
+                               output_names=["mask_file"],
+                               function=merge_tissues),
+        params=parse_key(params, "merge_brain_tissues"),
+        name="keep_GCC_brain")
+
+    IsoSurface_brain_pipe.connect(inputnode, 'segmented_file',
+                                  merge_brain_tissues, 'dseg_file')
+
+    # bin mask
+    bin_mask = pe.Node(interface=fsl.UnaryMaths(), name="bin_mask")
+    bin_mask.inputs.operation = "bin"
+
+    IsoSurface_brain_pipe.connect(merge_brain_tissues,
+                                  'mask_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")
+
+    IsoSurface_brain_pipe.connect(bin_mask, 'out_file', wmgm2mesh, "nii_file")
+
+    # outputnode
+    outputnode = pe.Node(
+        niu.IdentityInterface(
+            fields=["wmgm_stl", "wmgm_nii"]),
+        name='outputnode')
+
+    IsoSurface_brain_pipe.connect(bin_mask, 'out_file', outputnode, "wmgm_nii")
+    IsoSurface_brain_pipe.connect(wmgm2mesh, 'stl_file',
+                                  outputnode, "wmgm_stl")
+
+    return IsoSurface_brain_pipe

workflows/params_segment_macaque_ants.json

@@ -90,7 +90,7 @@
         "export_5tt_pipe":
         {
         },
-        "nii2mesh_brain_pipe":
+        "IsoSurface_brain_pipe":
         {
             "merge_brain_tissues":
             {