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})
