def create_dmn_pipeline_step2(name="dmn_step2", auto_reorient=True): inputnode = pe.Node( interface=util.IdentityInterface(fields=[ # For the fiber tracking "subject_id", "dwi", "bvecs", "bvals", "single_fiber_mask", "wm_mask", "termination_mask", "registration_matrix_file", "registration_image_file", # For the connectivity workflow "fa", "md", "roi_file", "summary_images" ]), name="inputnode") outputnode = pe.Node(interface=util.IdentityInterface(fields=[ "fiber_odfs", "fiber_tracks_tck_dwi", "fiber_tracks_trk_t1", "connectivity_files", "connectivity_data", "summary_images" ]), name="outputnode") tracking = anatomically_constrained_tracking("tracking") connectivity = create_paired_tract_analysis_wf("connectivity") workflow = pe.Workflow(name=name) workflow.base_dir = name workflow.connect([(inputnode, tracking, [ ("subject_id", "inputnode.subject_id"), ("dwi", "inputnode.dwi"), ("bvecs", "inputnode.bvecs"), ("bvals", "inputnode.bvals"), ("single_fiber_mask", "inputnode.single_fiber_mask"), ("wm_mask", "inputnode.wm_mask"), ("termination_mask", "inputnode.termination_mask"), ("registration_matrix_file", "inputnode.registration_matrix_file"), ("registration_image_file", "inputnode.registration_image_file"), ])]) workflow.connect([(tracking, connectivity, [ ("outputnode.fiber_tracks_tck_dwi", "inputnode.track_file") ])]) workflow.connect([(inputnode, connectivity, [ ("subject_id", "inputnode.subject_id"), ("fa", "inputnode.fa"), ("md", "inputnode.md"), ("roi_file", "inputnode.roi_file"), ("registration_matrix_file", "inputnode.registration_matrix_file"), ("registration_image_file", "inputnode.registration_image_file"), ])]) workflow.connect([(tracking, outputnode, [ ("outputnode.fiber_odfs", "fiber_odfs"), ("outputnode.fiber_tracks_tck_dwi", "fiber_tracks_tck_dwi"), ("outputnode.fiber_tracks_trk_t1", "fiber_tracks_trk_t1"), ])]) workflow.connect([(connectivity, outputnode, [ ("outputnode.connectivity_files", "connectivity_files"), ("outputnode.connectivity_data", "connectivity_data"), ("outputnode.summary_images", "summary_images"), ])]) return workflow
import os.path as op import nipype.interfaces.io as nio # Data i/o import nipype.interfaces.utility as util # utility import nipype.pipeline.engine as pe # pypeline engine import nipype.interfaces.fsl as fsl fsl.FSLCommand.set_default_output_type('NIFTI_GZ') from coma.workflows.dmn import create_paired_tract_analysis_wf path = op.abspath("/Users/erik/Dropbox/Thesis/Data/Bend1") short_roi_names = [ "LThal", "RThal", "LFront", "RFront", "LPrec", "RPrec", "LInfPar", "RInfPar" ] paired = create_paired_tract_analysis_wf("example_paired") paired.base_dir = op.abspath("example_paired") paired.inputs.inputnode.fa = op.join(path, "Bend1_fa.nii.gz") paired.inputs.inputnode.md = op.join(path, "Bend1_md.nii.gz") paired.inputs.inputnode.roi_file = op.join(path, "DMN_ROIs_DTIReg.nii") paired.inputs.inputnode.track_file = op.join(path, "Bend1_tracks_50k.tck") paired.inputs.inputnode.roi_names = short_roi_names paired.write_graph() paired.config['execution'] = { 'remove_unnecessary_outputs': 'false', 'hash_method': 'timestamp' } paired.run() #workflow.run(plugin='MultiProc', plugin_args={'n_procs' : 4})
import nipype.interfaces.utility as util # utility import nipype.pipeline.engine as pe # pypeline engine import nipype.interfaces.fsl as fsl fsl.FSLCommand.set_default_output_type('NIFTI_GZ') from coma.workflows.dmn import create_paired_tract_analysis_wf path = op.abspath("/Users/erik/Dropbox/Thesis/Data/Bend1") short_roi_names = ["LThal", "RThal", "LFront", "RFront", "LPrec", "RPrec", "LInfPar", "RInfPar"] paired = create_paired_tract_analysis_wf("example_paired") paired.base_dir = op.abspath("example_paired") paired.inputs.inputnode.fa = op.join(path,"Bend1_fa.nii.gz") paired.inputs.inputnode.md = op.join(path,"Bend1_md.nii.gz") paired.inputs.inputnode.roi_file = op.join(path,"DMN_ROIs_DTIReg.nii") paired.inputs.inputnode.track_file = op.join(path,"Bend1_tracks_50k.tck") paired.inputs.inputnode.roi_names = short_roi_names paired.write_graph() paired.config['execution'] = {'remove_unnecessary_outputs': 'false', 'hash_method': 'timestamp'} paired.run() #workflow.run(plugin='MultiProc', plugin_args={'n_procs' : 4})