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()
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,
scpreproc_alff)
nuisance_sink(workflow,
datasink,
nuisancepreproc,
func_in_mni)
if c.derivatives[0]:
"""
ALFF/fALFF
"""
workflow.connect(select_alff, 'outputspec.preprocessed_selector',
alffpreproc, 'inputspec.rest_res')
workflow.connect(funcpreproc, 'outputspec.preprocessed_mask',