diff --git a/examples/rsfmri_preprocessing.py b/examples/rsfmri_preprocessing.py index 2f28da277c..e9dcfad9af 100644 --- a/examples/rsfmri_preprocessing.py +++ b/examples/rsfmri_preprocessing.py @@ -33,15 +33,15 @@ specifically the 2mm versions of: -- `Joint Fusion Atlas `_ -- `MNI template `_ +- `Joint Fusion Atlas `_ +- `MNI template `_ The 2mm version was generated with:: >>> from nipype import freesurfer as fs >>> rs = fs.Resample() - >>> rs.inputs.in_file = 'OASIS-TRT-20_DKT31_CMA_jointfusion_labels_in_MNI152.nii.gz' - >>> rs.inputs.resampled_file = 'OASIS-TRT-20_DKT31_CMA_jointfusion_labels_in_MNI152_2mm.nii.gz' + >>> rs.inputs.in_file = 'OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152.nii.gz' + >>> rs.inputs.resampled_file = 'OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_2mm.nii.gz' >>> rs.inputs.voxel_size = (2., 2., 2.) >>> rs.inputs.args = '-rt nearest -ns 1' >>> res = rs.run() @@ -584,7 +584,7 @@ def create_workflow(files, reg.inputs.use_histogram_matching = [False] * 3 + [True] reg.inputs.output_warped_image = 'output_warped_image.nii.gz' reg.inputs.fixed_image = \ - os.path.abspath('OASIS-TRT-20_template_to_MNI152_2mm.nii.gz') + os.path.abspath('OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz') reg.inputs.num_threads = 4 reg.plugin_args = {'qsub_args': '-l nodes=1:ppn=4'} @@ -625,7 +625,7 @@ def create_workflow(files, sample2mni.inputs.interpolation = 'BSpline' sample2mni.inputs.invert_transform_flags = [False, False] sample2mni.inputs.reference_image = \ - os.path.abspath('OASIS-TRT-20_template_to_MNI152_2mm.nii.gz') + os.path.abspath('OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz') sample2mni.inputs.terminal_output = 'file' wf.connect(bandpass, 'out_file', sample2mni, 'input_image') wf.connect(merge, 'out', sample2mni, 'transforms') @@ -641,8 +641,8 @@ def create_workflow(files, ts2txt.inputs.indices = [8] + range(10, 14) + [17, 18, 26, 47] +\ range(49, 55) + [58] ts2txt.inputs.label_file = \ - os.path.abspath(('OASIS-TRT-20_DKT31_CMA_jointfusion_labels_in_MNI152' - '_2mm.nii.gz')) + os.path.abspath(('OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_' + '2mm.nii.gz')) wf.connect(sample2mni, 'output_image', ts2txt, 'timeseries_file') # Save the relevant data into an output directory @@ -699,7 +699,7 @@ def create_workflow(files, """ -def create_resting_workflow(args): +def create_resting_workflow(args, name='resting'): TR = args.TR slice_times = args.slice_times slice_thickness = None @@ -722,7 +722,8 @@ def create_resting_workflow(args): slice_thickness=slice_thickness, lowpass_freq=args.lowpass_freq, highpass_freq=args.highpass_freq, - sink_directory=os.path.abspath(args.sink)) + sink_directory=os.path.abspath(args.sink), + name=name) if args.field_maps: kwargs.update(**dict(fieldmap_images=args.field_maps, FM_TEdiff=args.TE_diff,