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# workflows.dmri.mrtrix.connectivity_mapping

## `create_connectivity_pipeline()`

Link to code

Creates a pipeline that does the same connectivity processing as in the dMRI: Connectivity - MRtrix, 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.mrtrix.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.networks
    outputnode.fa
    outputnode.struct
    outputnode.tracts
    outputnode.rois
    outputnode.odfs
    outputnode.filtered_tractography
    outputnode.tdi
    outputnode.nxstatscff
    outputnode.nxcsv
    outputnode.cmatrices_csv
    outputnode.mean_fiber_length
    outputnode.median_fiber_length
    outputnode.fiber_length_std

### Graph