From 9aaca3e2942e1eb1ba12068dc941d82f80e8b1ab Mon Sep 17 00:00:00 2001 From: ATAY Melvin Selim Date: Fri, 13 Dec 2024 14:43:13 +0100 Subject: [PATCH] everything team did not mention set to default- left blank --- narps_open/pipelines/team_L3V8.py | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) diff --git a/narps_open/pipelines/team_L3V8.py b/narps_open/pipelines/team_L3V8.py index 677eacee..f1cc6ec8 100644 --- a/narps_open/pipelines/team_L3V8.py +++ b/narps_open/pipelines/team_L3V8.py @@ -101,15 +101,9 @@ def get_preprocessing(self): motion_correction = Node(interface=Realign(), name='realign') motion_correction.inputs.register_to_mean = False # they registered to 1st slice - motion_correction.inputs.fwhm = 6 motion_correction.inputs.interp = 4 motion_correction.inputs.quality = 0.9 - motion_correction.inputs.separation = 4 - motion_correction.inputs.wrap = [0, 0, 0] - motion_correction.inputs.write_which = [2, 1] motion_correction.inputs.write_interp = 4 - motion_correction.inputs.write_wrap = [0, 0, 0] - motion_correction.inputs.write_mask = True motion_correction.inputs.jobtype = 'estwrite' @@ -124,10 +118,8 @@ def get_preprocessing(self): coregisteration = Node(Coregister(), name="coregister") coregisteration.inputs.jobtype = 'estimate' coregisteration.inputs.cost_function = 'nmi' - coregisteration.inputs.fwhm = [6.0, 6.0] - coregisteration.inputs.separation = [4.0, 2.0] - coregisteration.inputs.tolerance = [0.02, 0.02, 0.02, 0.001, 0.001, 0.001, 0.01, 0.01, 0.01, 0.001, 0.001, 0.001] + # connect coreg preprocessing.connect( motion_correction, 'mean_image', coregisteration, 'target') # target=mean preprocessing.connect( gunzip_anat, 'out_file', coregisteration, 'source') # T1w=source anat @@ -141,8 +133,6 @@ def get_preprocessing(self): segmentation.inputs.write_deformation_fields = [True, True] segmentation.inputs.channel_info = (0.0001, 60, (True, True)) segmentation.inputs.affine_regularization = 'mni' - segmentation.inputs.warping_regularization = [0, 0.001, 0.5, 0.05, 0.2] - segmentation.inputs.sampling_distance = 3 segmentation.inputs.tissues = [ [(spm_tissues_file, 1), 1, (True,False), (True, False)], [(spm_tissues_file, 2), 1, (True,False), (True, False)], @@ -162,7 +152,6 @@ def get_preprocessing(self): normalization = Node(Normalize12(), name="normalize") normalization.inputs.jobtype = 'write' - normalization.inputs.write_voxel_sizes = [3, 3, 3] normalization.inputs.write_interp = 4 normalization.inputs.warping_regularization = [0, 0.001, 0.5, 0.05, 0.2]