added rigid_flag (#276)

* added rigid_flag * remove pre_crop and crop
Macatools · Dec 12, 2024 · e58ce81 · e58ce81
1 parent 51eab60
commit e58ce81
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 16 deletions.
diff --git a/examples_doc/params_general_preparation.json b/examples_doc/params_general_preparation.json
@@ -59,15 +59,7 @@
 
     	"crop_aladin_pipe":
     	{
-            "pre_crop_z_T1":
-            {
-
-                "comment": "OPTIONAL",
-                "comment": "use with caution",
-                "params": "RobustFOV (FSL)",
-
-                "brainsize": "70"
-            },
+            "remove_capsule_pipe":{},
             "reg_T1_on_template":
             {
                 "params": "RegAladin (NiftyReg)"
@@ -80,13 +72,6 @@
 
                 "params": "RegAladin (NiftyReg)"
 
-            },
-            "crop_z_T1":
-            {
-                "comment": "OPTIONAL",
-                "params": "RobustFOV (FSL)",
-
-                "brainsize": "70"
             }
         },
 

diff --git a/macapype/pipelines/prepare.py b/macapype/pipelines/prepare.py
@@ -225,6 +225,7 @@ def create_short_preparation_pipe(params, params_template={},
     if 'aladin_T2_on_T1' in params.keys():
 
         align_T2_on_T1 = pe.Node(reg.RegAladin(), name="align_T2_on_T1")
+        align_T2_on_T1.inputs.rig_only_flag = True
 
         if "avg_reorient_pipe" in params.keys():
             data_preparation_pipe.connect(av_T1, 'outputnode.std_img',