From 5858fa72e0e7856ba33bcc1b9d41476a7a0e9793 Mon Sep 17 00:00:00 2001
From: David Meunier <david_meunier_79@hotmail.fr>
Date: Thu, 20 Jun 2024 16:35:56 +0200
Subject: [PATCH] t1_skull_fov + angio_pipe

---
 .../params_segment_macaque_ants_skull.json    | 96 ++++++++-----------
 1 file changed, 38 insertions(+), 58 deletions(-)

diff --git a/workflows/params_segment_macaque_ants_skull.json b/workflows/params_segment_macaque_ants_skull.json
index 26bf004..18a30f2 100755
--- a/workflows/params_segment_macaque_ants_skull.json
+++ b/workflows/params_segment_macaque_ants_skull.json
@@ -7,16 +7,12 @@
     {
 
         "aladin_T2_on_T1":{},
-        "crop_aladin_pipe":
-        {
-            "pre_crop_z_T1":
-            {
-                "brainsize": 70
-            },
+    	"crop_aladin_pipe":
+    	{
             "reg_T1_on_template":
             {
             }
-        },
+    	},
         "pad_template":
         {
             "copy_header" : true,
@@ -47,7 +43,7 @@
     },
     "debias":
     {
-        "s": 2
+        "s": 4
     },
     "brain_segment_pipe":
     {
@@ -173,77 +169,61 @@
         {
             "kernel_shape": "boxv",
             "kernel_size": 4.0
+        },
+        "t1_skull_fov":
+        {
+            "brainsize": 45
         }
     },
     "skull_ct_pipe":
-    {
-        "ct_skull_auto_mask":
-        {
-            "kmeans": true,
-            "sample_bins": 30,
-            "distance": 10,
-            "operation": "lower",
-            "index": 2
-        },
-        "ct_skull_dilate":
         {
-            "operation" : "modal",
-            "kernel_shape" : "boxv",
-            "kernel_size" : 3.0
-        },
-        "ct_skull_erode":
-        {
-            "kernel_shape" : "boxv",
-            "kernel_size" : 3.0
-        },
-        "ct_skull_fov":
-        {
-            "brainsize" : 65
-        }
+            "ct_skull_auto_mask":
+            {
+                "kmeans": false,
+                "sample_bins": 30,
+                "distance": 10,
+            	"operation": "higher",
+            	"index": 3
+            },
+            "ct_skull_dilate":
+            {
+                "operation" : "modal",
+                "kernel_shape" : "boxv",
+                "kernel_size" : 3.0
+            },
+            "ct_skull_erode":
+            {
+                "kernel_shape" : "boxv",
+                "kernel_size" : 3.0
+            },
+            "ct_skull_fov":
+            {
+                "brainsize" : 65
+            }
     },
     "angio_pipe":
     {
-        "denoise":
+        "angio_denoise":
         {
-            "s": 1,
+            "shrink_factor": 1
         },
-        "petra_head_dilate":
-        {
-            "operation": "modal",
-            "kernel_shape": "boxv",
-            "kernel_size": 7.0
-        },
-        "petra_head_erode":
-        {
-            "kernel_shape": "boxv",
-            "kernel_size": 7.0
-        },
-        "petra_fast":
+        "angio_fast":
         {
             "args": " -l 10",
             "img_type": 3,
             "output_biascorrected": true,
             "output_biasfield": true
         },
-        "petra_head_erode_skin":
-        {
-            "kernel_shape": "boxv",
-            "kernel_size": 12.0
-        },
-        "petra_skull_dilate":
+        "angio_dilate":
         {
             "operation": "modal",
             "kernel_shape": "boxv",
-            "kernel_size": 7.0
+            "kernel_size": 5.0
         },
-        "petra_skull_erode":
+        "angio_erode":
         {
             "kernel_shape": "boxv",
-            "kernel_size": 7.0
-        },
-        "petra_skull_fov":
-        {
-            "brainsize": 45
+            "kernel_size": 5.0
         }
     }
 }