From e58ce8184a39ac5bab3f2a964c232c7c9736d749 Mon Sep 17 00:00:00 2001
From: David Meunier <david_meunier_79@hotmail.fr>
Date: Thu, 12 Dec 2024 11:28:45 +0100
Subject: [PATCH] added rigid_flag (#276)

* added rigid_flag

* remove pre_crop and crop
---
 examples_doc/params_general_preparation.json | 17 +----------------
 macapype/pipelines/prepare.py                |  1 +
 2 files changed, 2 insertions(+), 16 deletions(-)

diff --git a/examples_doc/params_general_preparation.json b/examples_doc/params_general_preparation.json
index 94449d37..0ecdbe39 100644
--- 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
index 9eb0b427..4380dc63 100644
--- 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',