Add parcel

workflows/params_segment_marmo_ants_4animal_skull.json

@@ -1,7 +1,7 @@
 {
     "general":
     {
-        "template_name": "MBM_v3.0.1_6seg_stereoINT"
+        "template_name": "template_MBM_space-stereoINTv2"
     },
     "short_preparation_pipe":
     {
@@ -17,14 +17,6 @@
                 "rig_only_flag":true
             }
         },
-        "pad_template":
-        {
-            "operation" : "PadImage",
-            "op2" : "90"
-        },
-        "denoise":
-        {
-        },
         "fast":
         {
             "args": "-l 3"
@@ -45,16 +37,12 @@
     },
     "brain_segment_pipe":
     {
-        "reg":
+        "reg_f3d":
         {
-            "n": 2,
-            "m": "ref",
-            "dof": 12
         },
         "segment_atropos_pipe":
         {
             "use_priors":0.0,
-
             "Atropos":
             {
                 "dimension": 3
@@ -66,7 +54,9 @@
                 "wm": 3,
                 "csf": 4
             }
-        }
+        },
+        "parcel_gm":
+        {}
     },
     "export_5tt_pipe":
     {

workflows/segment_skull.py

@@ -376,6 +376,18 @@ def create_main_workflow(cmd, data_dir, process_dir, soft, species, subjects,
                 "Could not find template_seg {}".format(template_seg)
             params_template["template_seg"] = template_seg
 
+        elif len(template_files) == 4:
+
+            template_seg = os.path.join(template_path, template_files[2])
+            assert os.path.exists(template_seg), \
+                "Could not find template_seg {}".format(template_seg)
+            params_template["template_seg"] = template_seg
+
+            template_parcel = os.path.join(template_path, template_files[3])
+            assert os.path.exists(template_parcel), \
+                "Could not find template_parcel {}".format(template_parcel)
+            params_template["template_parcel"] = template_parcel
+
         elif len(template_files) == 5:
 
             template_gm = os.path.join(template_path, template_files[2])