workflows.dmri.camino.connectivity_mapping

create_connectivity_pipeline()

Link to code

Creates a pipeline that does the same connectivity processing as in the dMRI: Connectivity - Camino, CMTK, FreeSurfer example script. Given a subject id (and completed Freesurfer reconstruction) diffusion-weighted image, b-values, and b-vectors, the workflow will return the subject’s connectome as a Connectome File Format (CFF) file for use in Connectome Viewer (http://www.cmtk.org).

Example

>>> from nipype.workflows.dmri.camino.connectivity_mapping import create_connectivity_pipeline
>>> conmapper = create_connectivity_pipeline("nipype_conmap")
>>> conmapper.inputs.inputnode.subjects_dir = '.'
>>> conmapper.inputs.inputnode.subject_id = 'subj1'
>>> conmapper.inputs.inputnode.dwi = 'data.nii.gz'
>>> conmapper.inputs.inputnode.bvecs = 'bvecs'
>>> conmapper.inputs.inputnode.bvals = 'bvals'
>>> conmapper.run()                 

Inputs:

inputnode.subject_id
inputnode.subjects_dir
inputnode.dwi
inputnode.bvecs
inputnode.bvals
inputnode.resolution_network_file

Outputs:

outputnode.connectome
outputnode.cmatrix
outputnode.gpickled_network
outputnode.fa
outputnode.struct
outputnode.trace
outputnode.tracts
outputnode.tensors

Graph