Merge branch 'main' of github.com:Macatools/skullTo3d

# Conflicts: # .github/workflows/build_on_prerelease.yml
Macatools · Feb 9, 2024 · a8e9f25 · a8e9f25
2 parents fd0c1a7 + cca2f30
commit a8e9f25
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Showing 2 changed files with 7 additions and 9 deletions.
diff --git a/.github/workflows/build_on_prerelease.yml b/.github/workflows/build_on_prerelease.yml
@@ -96,7 +96,7 @@ jobs:
 
       - name: Running all test pipelines (ANTS cenir macaque petra)
         run: |
-            docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI:/data macatools/skullto3d:latest segment_skull -data /data/cenir-macaque-petra -out /data/cenir-macaque-petra/results -soft ANTS_prep_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad
+            docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI:/data macatools/skullto3d:latest segment_skull -data /data/cenir-macaque-petra -out /data/cenir-macaque-petra/results -soft ANTS_prep_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad -nprocs 1
 
             ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results
 
@@ -105,7 +105,7 @@ jobs:
             ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results/derivatives/macapype_crop_aladin_ants_skull_t1_petra_brain_t1_t2/sub-Magneto/anat
 
       - name: Cleaning dataset
-        run:
+        run: |
             sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results/derivatives/macapype_crop_aladin_ants_skull_t1_petra_brain_t1_t2
 
             sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/result/macapype_crop_aladin_ants_skull_t1_petra_brain_t1_t2
@@ -152,7 +152,7 @@ jobs:
             ls /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results/derivatives/macapype_crop_aladin_ants_skull_t1_CT_brain_t1_t2/sub-Marvin/ses-01/anat
 
       - name: Cleaning dataset
-        run:
+        run: |
             sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results/derivatives/macapype_crop_aladin_ants_skull_t1_CT_brain_t1_t2
 
             sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/result/macapype_crop_aladin_ants_skull_t1_CT_brain_t1_t2
@@ -188,7 +188,7 @@ jobs:
             echo ""
 
 
-      - name: Running all test pipelines (ANTS cerimed macaque CT)
+      - name: Running all test pipelines (ANTS cerimed marmo petra)
         run: |
             docker run -i -v /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI:/data macatools/skullto3d:latest segment_skull -data /data/cerimed-marmo-petra -out /data/results -soft ANTS_noseg_skull -species marmo -sub Paolina -ses 01 -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad
 
@@ -200,7 +200,7 @@ jobs:
 
 
       - name: Cleaning dataset
-        run:
+        run: |
             sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/results/derivatives/macapype_crop_aladin_ants_skull_t1_petra_brain_t1_t2
 
             sudo rm -rf /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/result/macapype_crop_aladin_ants_skull_t1_petra_brain_t1_t2

diff --git a/skullTo3d/pipelines/skull_pipe.py b/skullTo3d/pipelines/skull_pipe.py
@@ -24,8 +24,7 @@
 
 from macapype.nodes.prepare import average_align
 
-from macapype.nodes.surface import (keep_gcc,
-                                    wrap_nii2mesh_old, wrap_afni_IsoSurface)
+from macapype.nodes.surface import (keep_gcc, wrap_afni_IsoSurface)
 
 from skullTo3d.nodes.skull import (
     mask_auto_img)
@@ -773,7 +772,6 @@ def create_skull_petra_pipe(name="skull_petra_pipe", params={}):
     mesh_petra_skull = pe.Node(
         interface=niu.Function(input_names=["nii_file"],
                                output_names=["stl_file"],
-                               # function=wrap_nii2mesh_old),
                                function=wrap_afni_IsoSurface),
         name="mesh_petra_skull")
 
@@ -806,7 +804,7 @@ def create_skull_petra_pipe(name="skull_petra_pipe", params={}):
         mesh_robustpetra_skull = pe.Node(
             interface=niu.Function(input_names=["nii_file"],
                                    output_names=["stl_file"],
-                                   function=wrap_nii2mesh_old),
+                                   function=wrap_afni_IsoSurface),
             name="mesh_robustpetra_skull")
 
         skull_petra_pipe.connect(petra_skull_clean, "gcc_nii_file",