def prep_workflow(sub, rest_session_list, anat_session_list, seed_list, c): wfname = 'resting_preproc_sge' workflow = pe.Workflow(name=wfname) workflow.base_dir = c.workingDirectory workflow.crash_dir = c.crashLogDirectory workflow.config['execution'] = {'hash_method': 'timestamp'} """ BASIC and ALL preprocessing paths implemented below """ """ grab the subject data """ flowAnatFunc = create_anat_func_dataflow(sub, rest_session_list, anat_session_list, c.subjectDirectory, c.anatTemplate, c.funcTemplate, c.anatTemplateList, c.funcTemplateList) if c.derivatives[6]: """ grab the Group Analysis Data """ modelist, dervlist, labelist, template_dict, template_args = getGroupAnalysisInputs(c) gp_flow = create_gp_dataflow(c.sinkDirectory, modelist, dervlist, labelist, template_dict, template_args, 'gpflow') if c.derivatives[1]: """ grab the seeds data """ seedFlow = create_seed_dataflow(c.seedFile) if c.derivatives[4]: """ grab parcellation data for time series extraction """ pflow = create_parc_dataflow(c.unitDefinitionsDirectory) if c.derivatives[5]: pflow = create_parc_dataflow(c.unitDefinitionsDirectory) if c.derivatives[5]: """ grab mask data for time series extraction """ mflow = create_mask_dataflow(c.voxelMasksDirectory) """ Define workflows and set parameters """ anatpreproc = get_workflow('anat', c) funcpreproc = get_workflow('func', c) regpreproc = get_workflow('reg', c) segpreproc = get_workflow('seg', c) scpreproc = get_workflow('sc', c) select = get_workflow('select', c) nuisancepreproc = get_workflow('nuisance', c) mprage_mni = get_workflow('mprage_in_mnioutputs', c) func_in_mni = get_workflow('func_in_mnioutputs', c) freq_filter = get_workflow('freq_filter', c) if c.derivatives[0]: alffpreproc = get_workflow('alff', c) if c.derivatives[1]: scapreproc = get_workflow('sca', c) if c.derivatives[2]: vmhcpreproc = get_workflow('vmhc', c) if c.derivatives[4] or c.derivatives[5]: tspreproc = get_workflow('ts', c) if c.derivatives[6]: gppreproc = get_workflow('group_analysis', c) """ Calling datasink """ datasink = create_datasink(c.sinkDirectory) workflow.connect(flowAnatFunc, 'inputnode.subject_id', datasink, 'container') """ Make Connections """ workflow.connect(flowAnatFunc, 'datasource.anat', anatpreproc, 'inputspec.anat') workflow.connect(flowAnatFunc, 'datasource.rest', funcpreproc, 'inputspec.rest') workflow.connect(funcpreproc, 'outputspec.example_func', regpreproc, 'inputspec.example_func') workflow.connect(anatpreproc, 'outputspec.brain', regpreproc, 'inputspec.brain') workflow.connect(anatpreproc, 'outputspec.reorient', regpreproc, 'inputspec.reorient') workflow.connect(funcpreproc, 'outputspec.preprocessed_mask', segpreproc, 'inputspec.preprocessed_mask') workflow.connect(anatpreproc, 'outputspec.brain', segpreproc, 'inputspec.brain') workflow.connect(funcpreproc, 'outputspec.example_func', segpreproc, 'inputspec.example_func') workflow.connect(regpreproc, 'outputspec.highres2example_func_mat', segpreproc, 'inputspec.highres2example_func_mat') workflow.connect(regpreproc, 'outputspec.stand2highres_warp', segpreproc, 'inputspec.stand2highres_warp') workflow.connect(segpreproc, 'outputspec.wm_mask', nuisancepreproc, 'inputspec.wm_mask') workflow.connect(segpreproc, 'outputspec.csf_mask', nuisancepreproc, 'inputspec.csf_mask') workflow.connect(segpreproc, 'outputspec.gm_mask', nuisancepreproc, 'inputspec.gm_mask') """ Get T1 outputs in MNI """ workflow.connect(regpreproc, 'outputspec.highres2standard_warp', mprage_mni, 'inputspec.highres2standard_warp') workflow.connect(anatpreproc, 'outputspec.reorient', mprage_mni, 'inputspec.reorient') workflow.connect(anatpreproc, 'outputspec.brain', mprage_mni, 'inputspec.brain') workflow.connect(segpreproc, 'outputspec.probability_maps', mprage_mni, 'inputspec.probability_maps') workflow.connect(segpreproc, 'outputspec.mixeltype', mprage_mni, 'inputspec.mixeltype') workflow.connect(segpreproc, 'outputspec.partial_volume_map', mprage_mni, 'inputspec.partial_volume_map') workflow.connect(segpreproc, 'outputspec.partial_volume_files', mprage_mni, 'inputspec.partial_volume_files') """ Nuisance """ workflow.connect(funcpreproc, 'outputspec.preprocessed', nuisancepreproc, 'inputspec.realigned_file') workflow.connect(funcpreproc, 'outputspec.movement_parameters', nuisancepreproc, 'inputspec.motion_components') if(c.nuisanceBandpassFreq): workflow.connect(nuisancepreproc, 'outputspec.residual_file', freq_filter, 'realigned_file') workflow.connect(freq_filter, 'bandpassed_file', scpreproc, 'inputspec.preprocessed') workflow.connect(freq_filter, 'bandpassed_file', select, 'inputspec.preprocessed') else: workflow.connect(nuisancepreproc, 'outputspec.residual_file', scpreproc, 'inputspec.preprocessed') workflow.connect(nuisancepreproc, 'outputspec.residual_file', select, 'inputspec.preprocessed') workflow.connect(flowAnatFunc, 'datasource.rest', scpreproc, 'inputspec.rest') workflow.connect(funcpreproc, 'outputspec.movement_parameters', scpreproc, 'inputspec.movement_parameters') workflow.connect(scpreproc, 'outputspec.scrubbed_preprocessed', select, 'inputspec.scrubbed_preprocessed') workflow.connect(funcpreproc, 'outputspec.movement_parameters', select, 'inputspec.movement_parameters') workflow.connect(scpreproc, 'outputspec.scrubbed_movement_parameters', select, 'inputspec.scrubbed_movement_parameters') """ Get Func outputs in MNI """ workflow.connect(regpreproc, 'outputspec.highres2standard_warp', func_in_mni, 'inputspec.highres2standard_warp') workflow.connect(regpreproc, 'outputspec.example_func2highres_mat', func_in_mni, 'inputspec.premat') workflow.connect(funcpreproc, 'outputspec.preprocessed_mask', func_in_mni, 'inputspec.preprocessed_mask') workflow.connect(select, 'outputspec.preprocessed_selector', func_in_mni, 'inputspec.residual_file') anat_sink(workflow, datasink, mprage_mni) func_sink(workflow, datasink, funcpreproc, func_in_mni) reg_sink(workflow, datasink, regpreproc) seg_sink(workflow, datasink, segpreproc, mprage_mni) scrubbing_sink(workflow, datasink, scpreproc) nuisance_sink(workflow, datasink, nuisancepreproc) if c.derivatives[0]: """ ALFF/fALFF """ workflow.connect(select, 'outputspec.preprocessed_selector', alffpreproc, 'inputspec.rest_res') workflow.connect(funcpreproc, 'outputspec.preprocessed_mask', alffpreproc, 'inputspec.rest_mask') workflow.connect(func_in_mni, 'outputspec.preprocessed_mask_mni', alffpreproc, 'inputspec.rest_mask2standard') workflow.connect(regpreproc, 'outputspec.example_func2highres_mat', alffpreproc, 'inputspec.premat') workflow.connect(regpreproc, 'outputspec.highres2standard_warp', alffpreproc, 'inputspec.fieldcoeff_file') alff_sink(workflow, datasink, alffpreproc) if c.derivatives[1]: """ SCA (Seed Based Correlation Analysis) """ workflow.connect(seedFlow, 'out_file', scapreproc, 'seed_list_input.seed_list') workflow.connect(regpreproc, 'outputspec.example_func2highres_mat', scapreproc, 'inputspec.premat') workflow.connect(select, 'outputspec.preprocessed_selector', scapreproc, 'inputspec.residual_file') workflow.connect(select, 'outputspec.preprocessed_selector', scapreproc, 'inputspec.rest_res_filt') workflow.connect(regpreproc, 'outputspec.highres2standard_warp', scapreproc, 'inputspec.fieldcoeff_file') workflow.connect(func_in_mni, 'outputspec.preprocessed_mask_mni', scapreproc, 'inputspec.rest_mask2standard') sca_sink(workflow, datasink, scapreproc) if c.derivatives[2]: """ VMHC (Voxel-Mirrored Homotopic Connectivity) """ workflow.connect(nuisancepreproc, 'outputspec.residual_file', vmhcpreproc, 'inputspec.rest_res') workflow.connect(anatpreproc, 'outputspec.reorient', vmhcpreproc, 'inputspec.reorient') workflow.connect(anatpreproc, 'outputspec.brain', vmhcpreproc, 'inputspec.brain') workflow.connect(regpreproc, 'outputspec.example_func2highres_mat', vmhcpreproc, 'inputspec.example_func2highres_mat') vmhc_sink(workflow, datasink, vmhcpreproc) """ Time Series Extraction, Voxel Based and Vertices based Generates CSV and NUMPY files """ if c.derivatives[4] or c.derivatives[5]: workflow.connect(anatpreproc, 'outputspec.brain', tspreproc, 'inputspec.brain') workflow.connect(anatpreproc, 'outputspec.reorient', tspreproc, 'inputspec.reorient') workflow.connect(funcpreproc, 'outputspec.motion_correct', tspreproc, 'inputspec.motion_correct') workflow.connect(regpreproc, 'outputspec.highres2standard_warp', tspreproc, 'inputspec.warp_file') workflow.connect(regpreproc, 'outputspec.example_func2highres_mat', tspreproc, 'inputspec.premat') workflow.connect(pflow, 'out_file', tspreproc, 'getparc.parcelations') workflow.connect(mflow, 'out_file', tspreproc, 'getmask.masks') timeseries_sink(workflow, datasink, tspreproc, c.runSurfaceRegistraion) """ FSL Group Analysis """ if c.derivatives[6]: workflow.connect(gp_flow, 'gpflow.mat', gppreproc, 'inputspec.mat_file') workflow.connect(gp_flow, 'gpflow.con', gppreproc, 'inputspec.con_file') workflow.connect(gp_flow, 'gpflow.fts', gppreproc, 'inputspec.fts_file') workflow.connect(gp_flow, 'gpflow.grp', gppreproc, 'inputspec.grp_file') workflow.connect(gp_flow, 'gpflow.derv', gppreproc, 'inputspec.zmap_files') gp_datasink = create_gp_datasink(c.sinkDirectory) workflow.connect(gp_flow, 'inputnode.label', gp_datasink, 'container') group_analysis_sink(workflow, gp_datasink, gppreproc) if(not c.runOnGrid): workflow.run(plugin='MultiProc', plugin_args={'n_procs': c.numCoresPerSubject}) else: template_str = """ #!/bin/bash #$ -S /bin/bash #$ -V """ workflow.run(plugin='SGE', plugin_args=dict(qsub_args=c.qsubArgs, template=template_str)) workflow.write_graph()
def prep_workflow(sub, rest_session_list, anat_session_list, seed_list, c): wfname = 'resting_preproc_sge_OHSU' workflow = pe.Workflow(name=wfname) workflow.base_dir = c.workingDirectory workflow.crash_dir = c.crashLogDirectory workflow.config['execution'] = {'hash_method': 'timestamp'} """ BASIC and ALL preprocessing paths implemented below """ """ grab the subject data """ flowAnatFunc = create_anat_func_dataflow(sub, rest_session_list, anat_session_list, c.subjectDirectory, c.anatTemplate, c.funcTemplate, c.anatTemplateList, c.funcTemplateList) if c.derivatives[1]: """ grab the seeds data """ seedFlow = create_seed_dataflow(c.seedFile) if c.derivatives[4]: """ grab parcellation data for time series extraction """ pflow = create_parc_dataflow(c.unitDefinitionsDirectory) if c.derivatives[5]: pflow = create_parc_dataflow(c.unitDefinitionsDirectory) if c.derivatives[5]: """ grab mask data for time series extraction """ mflow = create_mask_dataflow(c.voxelMasksDirectory) """ Define workflows and set parameters """ anatpreproc = get_workflow('anat', c) funcpreproc = get_workflow('func', c) regpreproc = get_workflow('reg', c) segpreproc = get_workflow('seg', c) scpreproc = get_workflow('sc', c) pmpreproc = get_workflow('pm', c) select = get_workflow('select', c) nuisancepreproc = get_workflow('nuisance', c) mprage_mni = get_workflow('mprage_in_mnioutputs', c) func_in_mni = get_workflow('func_in_mnioutputs', c) freq_filter = get_workflow('freq_filter', c) TR_freq = pe.Node(util.Function(input_names=['in_files', 'TRa'], output_names=['TR'], function=getImgTR), name='TR_freq') TR_freq.inputs.TRa = c.TR if c.derivatives[0]: alffpreproc = get_workflow('alff', c) if c.derivatives[1]: scapreproc = get_workflow('sca', c) if c.derivatives[2]: vmhcpreproc = get_workflow('vmhc', c) if c.derivatives[4] or c.derivatives[5]: tspreproc = get_workflow('ts', c) """ Calling datasink """ datasink = create_datasink(c.sinkDirectory) workflow.connect(flowAnatFunc, 'inputnode.subject_id', datasink, 'container') """ Make Connections """ workflow.connect(flowAnatFunc, 'datasource.anat', anatpreproc, 'inputspec.anat') workflow.connect(flowAnatFunc, 'datasource.rest', funcpreproc, 'inputspec.rest') workflow.connect(funcpreproc, 'outputspec.example_func', regpreproc, 'inputspec.example_func') workflow.connect(anatpreproc, 'outputspec.brain', regpreproc, 'inputspec.brain') workflow.connect(anatpreproc, 'outputspec.reorient', regpreproc, 'inputspec.reorient') workflow.connect(funcpreproc, 'outputspec.preprocessed_mask', segpreproc, 'inputspec.preprocessed_mask') workflow.connect(anatpreproc, 'outputspec.brain', segpreproc, 'inputspec.brain') workflow.connect(funcpreproc, 'outputspec.example_func', segpreproc, 'inputspec.example_func') workflow.connect(regpreproc, 'outputspec.highres2example_func_mat', segpreproc, 'inputspec.highres2example_func_mat') workflow.connect(regpreproc, 'outputspec.stand2highres_warp', segpreproc, 'inputspec.stand2highres_warp') workflow.connect(flowAnatFunc, 'datasource.rest', pmpreproc, 'inputspec.rest') workflow.connect(funcpreproc, 'outputspec.movement_parameters', pmpreproc, 'inputspec.movement_parameters') workflow.connect(funcpreproc, 'outputspec.max_displacement', pmpreproc, 'inputspec.max_displacement') workflow.connect(segpreproc, 'outputspec.wm_mask', nuisancepreproc, 'inputspec.wm_mask') workflow.connect(segpreproc, 'outputspec.csf_mask', nuisancepreproc, 'inputspec.csf_mask') workflow.connect(segpreproc, 'outputspec.gm_mask', nuisancepreproc, 'inputspec.gm_mask') """ Get T1 outputs in MNI """ workflow.connect(regpreproc, 'outputspec.highres2standard_warp', mprage_mni, 'inputspec.highres2standard_warp') workflow.connect(anatpreproc, 'outputspec.reorient', mprage_mni, 'inputspec.reorient') workflow.connect(anatpreproc, 'outputspec.brain', mprage_mni, 'inputspec.brain') workflow.connect(segpreproc, 'outputspec.probability_maps', mprage_mni, 'inputspec.probability_maps') workflow.connect(segpreproc, 'outputspec.mixeltype', mprage_mni, 'inputspec.mixeltype') workflow.connect(segpreproc, 'outputspec.partial_volume_map', mprage_mni, 'inputspec.partial_volume_map') workflow.connect(segpreproc, 'outputspec.partial_volume_files', mprage_mni, 'inputspec.partial_volume_files') """ Nuisance """ workflow.connect(funcpreproc, 'outputspec.preprocessed', nuisancepreproc, 'inputspec.realigned_file') workflow.connect(funcpreproc, 'outputspec.movement_parameters', nuisancepreproc, 'inputspec.motion_components') if(c.nuisanceBandpass): workflow.connect(nuisancepreproc, 'outputspec.residual_file', TR_freq, 'in_files') workflow.connect(TR_freq, 'TR', freq_filter, 'sample_period') workflow.connect(nuisancepreproc, 'outputspec.residual_file', freq_filter, 'realigned_file') workflow.connect(freq_filter, 'bandpassed_file', scpreproc, 'inputspec.preprocessed') workflow.connect(freq_filter, 'bandpassed_file', select, 'inputspec.preprocessed') else: workflow.connect(nuisancepreproc, 'outputspec.residual_file', scpreproc, 'inputspec.preprocessed') workflow.connect(nuisancepreproc, 'outputspec.residual_file', select, 'inputspec.preprocessed') workflow.connect(pmpreproc, 'outputspec.frames_in_1D', scpreproc, 'inputspec.frames_in_1D') workflow.connect(funcpreproc, 'outputspec.movement_parameters', scpreproc, 'inputspec.movement_parameters') workflow.connect(scpreproc, 'outputspec.scrubbed_preprocessed', select, 'inputspec.scrubbed_preprocessed') workflow.connect(funcpreproc, 'outputspec.movement_parameters', select, 'inputspec.movement_parameters') workflow.connect(scpreproc, 'outputspec.scrubbed_movement_parameters', select, 'inputspec.scrubbed_movement_parameters') """ Get Func outputs in MNI """ workflow.connect(regpreproc, 'outputspec.highres2standard_warp', func_in_mni, 'inputspec.highres2standard_warp') workflow.connect(regpreproc, 'outputspec.example_func2highres_mat', func_in_mni, 'inputspec.premat') workflow.connect(funcpreproc, 'outputspec.preprocessed_mask', func_in_mni, 'inputspec.preprocessed_mask') workflow.connect(nuisancepreproc, 'outputspec.residual_file', func_in_mni, 'inputspec.residual_file') anat_sink(workflow, datasink, anatpreproc, mprage_mni) func_sink(workflow, datasink, funcpreproc, func_in_mni) reg_sink(workflow, datasink, regpreproc) seg_sink(workflow, datasink, segpreproc, mprage_mni) parameters_sink(workflow, datasink, pmpreproc) scrubbing_sink(workflow, datasink, scpreproc) nuisance_sink(workflow, datasink, nuisancepreproc, func_in_mni) if c.derivatives[0]: """ ALFF/fALFF """ workflow.connect(select, 'outputspec.preprocessed_selector', alffpreproc, 'inputspec.rest_res') workflow.connect(funcpreproc, 'outputspec.preprocessed_mask', alffpreproc, 'inputspec.rest_mask') workflow.connect(func_in_mni, 'outputspec.preprocessed_mask_mni', alffpreproc, 'inputspec.rest_mask2standard') workflow.connect(regpreproc, 'outputspec.example_func2highres_mat', alffpreproc, 'inputspec.premat') workflow.connect(regpreproc, 'outputspec.highres2standard_warp', alffpreproc, 'inputspec.fieldcoeff_file') alff_sink(workflow, datasink, alffpreproc) if c.derivatives[1]: """ SCA (Seed Based Correlation Analysis) """ workflow.connect(seedFlow, 'out_file', scapreproc, 'seed_list_input.seed_list') workflow.connect(regpreproc, 'outputspec.example_func2highres_mat', scapreproc, 'inputspec.premat') workflow.connect(select, 'outputspec.preprocessed_selector', scapreproc, 'inputspec.residual_file') workflow.connect(select, 'outputspec.preprocessed_selector', scapreproc, 'inputspec.rest_res_filt') workflow.connect(regpreproc, 'outputspec.highres2standard_warp', scapreproc, 'inputspec.fieldcoeff_file') workflow.connect(func_in_mni, 'outputspec.preprocessed_mask_mni', scapreproc, 'inputspec.rest_mask2standard') sca_sink(workflow, datasink, scapreproc) if c.derivatives[2]: """ VMHC (Voxel-Mirrored Homotopic Connectivity) """ workflow.connect(select, 'outputspec.preprocessed_selector', vmhcpreproc, 'inputspec.rest_res') workflow.connect(anatpreproc, 'outputspec.reorient', vmhcpreproc, 'inputspec.reorient') workflow.connect(anatpreproc, 'outputspec.brain', vmhcpreproc, 'inputspec.brain') workflow.connect(regpreproc, 'outputspec.example_func2highres_mat', vmhcpreproc, 'inputspec.example_func2highres_mat') vmhc_sink(workflow, datasink, vmhcpreproc) """ Time Series Extraction, Voxel Based and Vertices based Generates CSV and NUMPY files """ if c.derivatives[4] or c.derivatives[5]: workflow.connect(anatpreproc, 'outputspec.brain', tspreproc, 'inputspec.brain') workflow.connect(anatpreproc, 'outputspec.reorient', tspreproc, 'inputspec.reorient') workflow.connect(funcpreproc, 'outputspec.motion_correct', tspreproc, 'inputspec.motion_correct') workflow.connect(regpreproc, 'outputspec.highres2standard_warp', tspreproc, 'inputspec.warp_file') workflow.connect(regpreproc, 'outputspec.example_func2highres_mat', tspreproc, 'inputspec.premat') workflow.connect(pflow, 'out_file', tspreproc, 'getparc.parcelations') workflow.connect(mflow, 'out_file', tspreproc, 'getmask.masks') timeseries_sink(workflow, datasink, tspreproc, c.runSurfaceRegistraion) if(not c.runOnGrid): workflow.run(plugin='MultiProc', plugin_args={'n_procs': c.numCoresPerSubject}) else: template_str = """ #!/bin/bash #$ -S /bin/bash #$ -V """ workflow.run(plugin='SGE', plugin_args=dict(qsub_args=c.qsubArgs, template=template_str)) workflow.write_graph()
flowAnatFunc = create_anat_func_dataflow([sub], rest_session_list, anat_session_list, c.subjectDirectory, c.anatTemplate, c.funcTemplate, c.anatTemplateList, c.funcTemplateList) if c.derivatives[1]: """ grab the seeds data """ seedFlow = create_seed_dataflow(c.seedFile) if c.derivatives[4]: """ grab parcellation data for time series extraction """ pflow = create_parc_dataflow(c.unitDefinitionsDirectory) if c.derivatives[5]: pflow = create_parc_dataflow(c.unitDefinitionsDirectory) if c.derivatives[5]: """ grab mask data for time series extraction """ mflow = create_mask_dataflow(c.voxelMasksDirectory)