Created
May 25, 2017 10:37
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| import nipype.pipeline.engine as pe | |
| import nipype.interfaces.utility as util | |
| import nipype.interfaces.io as nio | |
| from nipype.interfaces.freesurfer import SampleToSurface | |
| '''directories''' | |
| preprocDir = "/scr/adenauer1/Franz/nki_nilearn" | |
| freesurferDir = "/scr/ilz2/nilearn_vol2surf_wd/freesurfer" | |
| workingDir = "/scr/ilz2/nilearn_vol2surf_wd/" | |
| sinkDir = "/scr/ilz1/nilearn_vol2surf_sink/" | |
| '''subjects''' | |
| subjects = [] | |
| with open('/scr/ilz1/nilearn_vol2surf_sink/subjects.txt') as f: | |
| subjects = f.read().splitlines() | |
| '''workflow''' | |
| if __name__ == '__main__': | |
| wf = pe.Workflow(name="map_to_surface") | |
| wf.base_dir = workingDir | |
| wf.config['execution']['crashdump_dir'] = wf.base_dir + "/crash_files" | |
| subjects_infosource = pe.Node(util.IdentityInterface(fields=['subject_id']), name="subjects_infosource") | |
| subjects_infosource.iterables = ('subject_id', subjects) | |
| hemi_infosource = pe.Node(util.IdentityInterface(fields=['hemi']), name="hemi_infosource") | |
| hemi_infosource.iterables = ('hemi', ['lh', 'rh']) | |
| datagrabber = pe.Node(nio.DataGrabber(infields=['subject_id'], | |
| outfields=['resting']), | |
| name="datagrabber") | |
| datagrabber.inputs.base_directory = preprocDir | |
| datagrabber.inputs.template = '%s/residual_filt_norm_warp.nii.gz' | |
| datagrabber.inputs.template_args['resting'] = [['subject_id']] | |
| datagrabber.inputs.sort_filelist = True | |
| datagrabber.inputs.raise_on_empty = False | |
| vol2surf = pe.Node(SampleToSurface(mni152reg=True, | |
| target_subject='fsaverage5', | |
| subjects_dir=freesurferDir, | |
| cortex_mask=True, | |
| sampling_method="average", | |
| sampling_range=(0.2, 0.8, 0.1), | |
| sampling_units="frac", | |
| smooth_surf=0.0, | |
| args="--out_type GIFTI"), | |
| name='vol2surf_lsd') | |
| def gen_out_file(subject_id, hemi): | |
| return "%s_%s_preprocessed_fsaverage5_fwhm0.gii" % (subject_id, hemi) | |
| output_name = pe.Node(util.Function(input_names=['subject_id', 'hemi'], | |
| output_names=['name'], | |
| function=gen_out_file), | |
| name="output_name") | |
| datasink = pe.Node(nio.DataSink(parameterization=False, base_directory=sinkDir), name='sinker') | |
| wf.connect([(subjects_infosource, datagrabber, [('subject_id', 'subject_id')]), | |
| (hemi_infosource, vol2surf, [('hemi', 'hemi')]), | |
| (subjects_infosource, output_name, [('subject_id', 'subject_id')]), | |
| (hemi_infosource, output_name, [('hemi', 'hemi')]), | |
| (datagrabber, vol2surf, [('resting', 'source_file')]), | |
| (output_name, vol2surf, [('name', 'out_file')]), | |
| (vol2surf, datasink, [('out_file', '@rest_surf')]) | |
| ]) | |
| wf.run() | |
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