simplified version (to be tested fully)

Macatools · Mar 4, 2024 · 6975f91 · 6975f91
1 parent 1b1ad1c
commit 6975f91
Showing 1 changed file with 26 additions and 30 deletions.
diff --git a/workflows/params_segment_marmo_ants_skull.json b/workflows/params_segment_marmo_ants_skull.json
@@ -1,13 +1,18 @@
 {
     "general":
     {
-         "template_name": "MBM_v3.0.1_6seg",
-         "template_stereo_name": "bma-1_0p2mm_padded"
+        "template_name": "MBM_v3.0.1_6seg",
+        "template_stereo_name": "bma-1_0p2mm",
+        "template_aladin_name": "bma-1_0p2mm"
     },
-    "short_preparation_pipe":
+     "short_preparation_pipe":
     {
-        "crop_aladin_T1":
+    	"crop_aladin_T1":
+    	{
+    	},
+        "crop_z_T1":
         {
+            "brainsize": 30
         }
     },
     "fast":
@@ -28,59 +33,50 @@
     },
     "debias":
     {
-        "s": 4,
-        "k": true
+        "s": 4
     },
     "brain_segment_pipe":
     {
-        "register_NMT_pipe": {},
+        "reg":
+        {
+            "n": 2,
+            "m": "ref",
+            "dof": 12
+        },
         "segment_atropos_pipe":
         {
-            "use_priors": 0.0,
+            "use_priors":0.0,
+
             "Atropos":
             {
                 "dimension": 3
             },
+
             "tissue_dict":
             {
-                "gm": [1, 2],
+                "gm": [1,2],
                 "wm": 3,
                 "csf": 4
             }
         },
-        "export_5tt_pipe": {},
-        "nii2mesh_brain_pipe":
+        "export_5tt_pipe":
+        {
+        },
+        "IsoSurface_brain_pipe":
         {
             "merge_brain_tissues":
             {
-                "keep_indexes": [1, 2, 3]
+                "keep_indexes": [1,2,3]
             }
         }
     },
     "native_to_stereo_pipe":
     {
-        "skull_stripped_template": true,
-        "use_T2": {},
-        "pad_template_T1":
-        {
-            "pad_val": 0
-        },
         "reg_T1_on_template":
         {
-            "nac_flag": true,
-            "rig_only_flag": true,
-            "nosym_flag": true,
-            "ln_val": 12,
-            "lp_val": 10,
-            "smoo_r_val": 1.0
         },
-        "reg_T1_on_template2":
+        "resample_T1_pad":
         {
-            "rig_only_flag": true,
-            "nosym_flag": true,
-            "ln_val": 17,
-            "lp_val": 15,
-            "smoo_r_val": 1.0
         }
     },
     "skull_petra_pipe":