From 6b8677055d4085257c762d7a4b9567e7bd353bb0 Mon Sep 17 00:00:00 2001 From: David Meunier Date: Tue, 10 Dec 2024 16:50:10 +0100 Subject: [PATCH 1/2] added rigid_flag --- macapype/pipelines/prepare.py | 1 + 1 file changed, 1 insertion(+) 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', From 753008d48bead2d36f6bd943142dee0dd91bcf29 Mon Sep 17 00:00:00 2001 From: David Meunier Date: Thu, 12 Dec 2024 11:15:58 +0100 Subject: [PATCH 2/2] remove pre_crop and crop --- examples_doc/params_general_preparation.json | 17 +---------------- 1 file changed, 1 insertion(+), 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" } },