Modif marmo ants skull (#33)

* removed_crop_z_T1; added head_stl
Macatools · Jan 23, 2025 · d25b481 · d25b481
1 parent 8458f71
commit d25b481
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Showing 3 changed files with 40 additions and 6 deletions.
diff --git a/skullTo3d/pipelines/rename.py b/skullTo3d/pipelines/rename.py
@@ -46,6 +46,22 @@ def rename_all_skull_petra_derivatives(params, main_workflow, segment_pnh_pipe,
             rename_stereo_petra_skull_mask, 'out_file',
             datasink, '@stereo_petra_skull_mask')
 
+        # rename petra_head_stl
+        rename_petra_head_stl = pe.Node(niu.Rename(),
+                                        name="rename_petra_head_stl")
+        rename_petra_head_stl.inputs.format_string = \
+            pref_deriv + "_desc-petra_headmask"
+        rename_petra_head_stl.inputs.parse_string = parse_str
+        rename_petra_head_stl.inputs.keep_ext = True
+
+        main_workflow.connect(
+            skull_petra_pipe, 'outputnode.petra_head_stl',
+            rename_petra_head_stl, 'in_file')
+
+        main_workflow.connect(
+            rename_petra_head_stl, 'out_file',
+            datasink, '@petra_head_stl')
+
         # rename stereo_petra_head_mask
         rename_stereo_petra_head_mask = pe.Node(
             niu.Rename(), name="rename_stereo_petra_head_mask")

diff --git a/skullTo3d/pipelines/skull_pipe.py b/skullTo3d/pipelines/skull_pipe.py
@@ -805,6 +805,14 @@ def create_autonomous_skull_petra_pipe(name="skull_petra_pipe", params={}):
         inputnode, ('indiv_params', parse_key, "petra_head_erode"),
         petra_head_erode, "indiv_params")
 
+    # mesh_petra_head #######
+    mesh_petra_head = pe.Node(
+        interface=IsoSurface(),
+        name="mesh_petra_head")
+
+    skull_petra_pipe.connect(petra_head_erode, "out_file",
+                             mesh_petra_head, "nii_file")
+
     # ### Masking with head mask
     # petra_hmasked ####### [okey]
     petra_hmasked = pe.Node(interface=ApplyMask(),
@@ -1033,7 +1041,7 @@ def create_autonomous_skull_petra_pipe(name="skull_petra_pipe", params={}):
         niu.IdentityInterface(
             fields=["petra_skull_mask", "petra_skull_stl",
                     "robustpetra_skull_mask", "robustpetra_skull_stl",
-                    "petra_head_mask"]),
+                    "petra_head_mask", "petra_head_stl"]),
         name='outputnode')
 
     skull_petra_pipe.connect(petra_head_erode, "out_file",
@@ -1042,6 +1050,9 @@ def create_autonomous_skull_petra_pipe(name="skull_petra_pipe", params={}):
     skull_petra_pipe.connect(mesh_petra_skull, "stl_file",
                              outputnode, "petra_skull_stl")
 
+    skull_petra_pipe.connect(mesh_petra_head, "stl_file",
+                             outputnode, "petra_head_stl")
+
     skull_petra_pipe.connect(petra_skull_erode, "out_file",
                              outputnode, "petra_skull_mask")
 
@@ -1260,6 +1271,14 @@ def create_skull_petra_pipe(name="skull_petra_pipe", params={}):
         inputnode, ('indiv_params', parse_key, "petra_head_erode"),
         petra_head_erode, "indiv_params")
 
+    # mesh_petra_head #######
+    mesh_petra_head = pe.Node(
+        interface=IsoSurface(),
+        name="mesh_petra_head")
+
+    skull_petra_pipe.connect(petra_head_erode, "out_file",
+                             mesh_petra_head, "nii_file")
+
     # ### Masking with head mask
     # petra_hmasked ####### [okey]
     petra_hmasked = pe.Node(interface=ApplyMask(),
@@ -1483,12 +1502,15 @@ def create_skull_petra_pipe(name="skull_petra_pipe", params={}):
         niu.IdentityInterface(
             fields=["petra_skull_mask", "petra_skull_stl",
                     "robustpetra_skull_mask", "robustpetra_skull_stl",
-                    "petra_head_mask"]),
+                    "petra_head_mask", "petra_head_stl"]),
         name='outputnode')
 
     skull_petra_pipe.connect(petra_head_erode, "out_file",
                              outputnode, "petra_head_mask")
 
+    skull_petra_pipe.connect(mesh_petra_head, "stl_file",
+                             outputnode, "petra_head_stl")
+
     skull_petra_pipe.connect(mesh_petra_skull, "stl_file",
                              outputnode, "petra_skull_stl")
 

diff --git a/workflows/params_segment_marmo_ants_skull.json b/workflows/params_segment_marmo_ants_skull.json
@@ -29,10 +29,6 @@
                 "ln_val": 17,
                 "lp_val": 15,
                 "smoo_r_val": 1.0
-            },
-            "crop_z_T1":
-            {
-                "brainsize": 30
             }
     	},
         "pad_template":