diff --git a/narps_open/pipelines/team_08MQ.py b/narps_open/pipelines/team_08MQ.py index f84fbb24..dc5c4aee 100644 --- a/narps_open/pipelines/team_08MQ.py +++ b/narps_open/pipelines/team_08MQ.py @@ -13,7 +13,7 @@ Threshold, Info, SUSAN, FLIRT, ApplyWarp, EpiReg, ApplyXFM, ConvertXFM ) from nipype.algorithms.confounds import CompCor -from nipype.interfaces.ants import Registration +from nipype.interfaces.ants import Registration, ApplyTransforms from narps_open.pipelines import Pipeline from narps_open.data.task import TaskInformation @@ -104,7 +104,7 @@ def get_preprocessing(self): normalization_anat.inputs.use_histogram_matching = True normalization_anat.inputs.winsorize_lower_quantile = 0.005 normalization_anat.inputs.winsorize_upper_quantile = 0.995 - normalization_anat.inputs.write_composite_transform = True + #normalization_anat.inputs.write_composite_transform = True # Threshold Node - create white-matter mask threshold_white_matter = Node(Threshold(), name = 'threshold_white_matter') @@ -185,8 +185,9 @@ def get_preprocessing(self): alignment_func_to_anat.inputs.apply_xfm = True # ApplyWarp Node - Alignment of functional data to MNI space - alignment_func_to_mni = Node(ApplyWarp(), name = 'alignment_func_to_mni') - alignment_func_to_mni.inputs.ref_file = Info.standard_image('MNI152_T1_2mm_brain.nii.gz') + alignment_func_to_mni = Node(ApplyTransforms(), name = 'alignment_func_to_mni') + alignment_func_to_mni.inputs.reference_image = \ + Info.standard_image('MNI152_T1_2mm_brain.nii.gz') # Merge Node - Merge the two masks (WM and CSF) in one input for the next node merge_masks = Node(Merge(2), name = 'merge_masks') @@ -257,8 +258,8 @@ def get_preprocessing(self): (slice_time_correction, alignment_func_to_anat, [('slice_time_corrected_file', 'in_file')]), (coregistration_sbref, alignment_func_to_anat, [('out_matrix_file', 'in_matrix_file')]), (brain_extraction_anat, alignment_func_to_anat, [('out_file', 'reference')]), - (alignment_func_to_anat, alignment_func_to_mni, [('out_file', 'in_file')]), - (normalization_anat, alignment_func_to_mni, [('composite_transform', 'field_file')]), + (alignment_func_to_anat, alignment_func_to_mni, [('out_file', 'input_image')]), + (normalization_anat, alignment_func_to_mni, [('forward_transforms', 'transforms')]), (merge_masks, compute_confounds, [('out', 'mask_files')]), # Masks are in the func space (slice_time_correction, compute_confounds, [('slice_time_corrected_file', 'realigned_file')]),