.. AUTO-GENERATED FILE -- DO NOT EDIT!

workflows.dmri.camino.connectivity_mapping
==========================================


.. module:: nipype.workflows.dmri.camino.connectivity_mapping


.. _nipype.workflows.dmri.camino.connectivity_mapping.create_connectivity_pipeline:

:func:`create_connectivity_pipeline`
------------------------------------

`Link to code <http://github.com/nipy/nipype/tree/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/workflows/dmri/camino/connectivity_mapping.py#L15>`__



Creates a pipeline that does the same connectivity processing as in the
:ref:`example_dmri_connectivity` 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()                 # doctest: +SKIP

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
~~~~~

.. graphviz::

	digraph connectivity{

	  label="connectivity";

	  connectivity_inputnode[label="inputnode (utility)"];

	  connectivity_outputnode[label="outputnode (utility)"];

	  subgraph cluster_connectivity_mapping {

	      label="mapping";

	    connectivity_mapping_inputnode_within[label="inputnode_within (utility)"];

	    connectivity_mapping_fsl2scheme[label="fsl2scheme (camino)"];

	    connectivity_mapping_fssourceLH[label="fssourceLH (io)"];

	    connectivity_mapping_mris_convertLH[label="mris_convertLH (freesurfer)"];

	    connectivity_mapping_mris_convertLHsphere[label="mris_convertLHsphere (freesurfer)"];

	    connectivity_mapping_mris_convertLHwhite[label="mris_convertLHwhite (freesurfer)"];

	    connectivity_mapping_mris_convertLHlabels[label="mris_convertLHlabels (freesurfer)"];

	    connectivity_mapping_mris_convertLHinflated[label="mris_convertLHinflated (freesurfer)"];

	    connectivity_mapping_bet_b0[label="bet_b0 (fsl)"];

	    connectivity_mapping_fssourceRH[label="fssourceRH (io)"];

	    connectivity_mapping_mris_convertRHsphere[label="mris_convertRHsphere (freesurfer)"];

	    connectivity_mapping_mris_convertRH[label="mris_convertRH (freesurfer)"];

	    connectivity_mapping_mris_convertRHinflated[label="mris_convertRHinflated (freesurfer)"];

	    connectivity_mapping_mris_convertRHwhite[label="mris_convertRHwhite (freesurfer)"];

	    connectivity_mapping_GiftiSurfaces[label="GiftiSurfaces (utility)"];

	    connectivity_mapping_image2voxel[label="image2voxel (camino)"];

	    connectivity_mapping_dtifit[label="dtifit (camino)"];

	    connectivity_mapping_trace[label="trace (camino)"];

	    connectivity_mapping_analyzeheader_trace[label="analyzeheader_trace (camino)"];

	    connectivity_mapping_trace2nii[label="trace2nii (misc)"];

	    connectivity_mapping_fa[label="fa (camino)"];

	    connectivity_mapping_analyzeheader_fa[label="analyzeheader_fa (camino)"];

	    connectivity_mapping_fa2nii[label="fa2nii (misc)"];

	    connectivity_mapping_dtlutgen[label="dtlutgen (camino)"];

	    connectivity_mapping_picopdfs[label="picopdfs (camino)"];

	    connectivity_mapping_track[label="track (camino)"];

	    connectivity_mapping_camino2trackvis[label="camino2trackvis (camino2trackvis)"];

	    connectivity_mapping_trk2camino[label="trk2camino (camino2trackvis)"];

	    connectivity_mapping_vtkstreamlines[label="vtkstreamlines (camino)"];

	    connectivity_mapping_dteig[label="dteig (camino)"];

	    connectivity_mapping_fssource[label="fssource (io)"];

	    connectivity_mapping_mri_convert_AparcAseg[label="mri_convert_AparcAseg (freesurfer)"];

	    connectivity_mapping_ROIGen_structspace[label="ROIGen_structspace (cmtk)"];

	    connectivity_mapping_CreateNodes[label="CreateNodes (cmtk)"];

	    connectivity_mapping_mri_convert_Brain[label="mri_convert_Brain (freesurfer)"];

	    connectivity_mapping_coregister[label="coregister (fsl)"];

	    connectivity_mapping_convertxfm[label="convertxfm (fsl)"];

	    connectivity_mapping_inverse_AparcAseg[label="inverse_AparcAseg (fsl)"];

	    connectivity_mapping_ROIGen[label="ROIGen (cmtk)"];

	    connectivity_mapping_CreateMatrix[label="CreateMatrix (cmtk)"];

	    connectivity_mapping_FiberDataArrays[label="FiberDataArrays (utility)"];

	    connectivity_mapping_NiftiVolumes[label="NiftiVolumes (utility)"];

	    connectivity_mapping_inverse[label="inverse (fsl)"];

	    connectivity_mapping_mris_convertRHlabels[label="mris_convertRHlabels (freesurfer)"];

	    connectivity_mapping_GiftiLabels[label="GiftiLabels (utility)"];

	    connectivity_mapping_CFFConverter[label="CFFConverter (cmtk)"];

	    connectivity_mapping_inputnode_within -> connectivity_mapping_fssource;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_fssource;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_fsl2scheme;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_fsl2scheme;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_analyzeheader_fa;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_analyzeheader_fa;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_CreateNodes;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_camino2trackvis;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_camino2trackvis;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_fssourceLH;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_fssourceLH;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_analyzeheader_trace;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_analyzeheader_trace;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_bet_b0;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_bet_b0;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_NiftiVolumes;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_image2voxel;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_fa2nii;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_CFFConverter;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_fssourceRH;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_fssourceRH;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_trace2nii;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_CreateMatrix;

	    connectivity_mapping_inputnode_within -> connectivity_mapping_CreateMatrix;

	    connectivity_mapping_fsl2scheme -> connectivity_mapping_dtifit;

	    connectivity_mapping_fsl2scheme -> connectivity_mapping_dtlutgen;

	    connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLH;

	    connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLHsphere;

	    connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLHwhite;

	    connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLHlabels;

	    connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLHlabels;

	    connectivity_mapping_fssourceLH -> connectivity_mapping_mris_convertLHinflated;

	    connectivity_mapping_mris_convertLH -> connectivity_mapping_GiftiSurfaces;

	    connectivity_mapping_mris_convertLHsphere -> connectivity_mapping_GiftiSurfaces;

	    connectivity_mapping_mris_convertLHwhite -> connectivity_mapping_GiftiSurfaces;

	    connectivity_mapping_mris_convertLHlabels -> connectivity_mapping_GiftiLabels;

	    connectivity_mapping_mris_convertLHinflated -> connectivity_mapping_GiftiSurfaces;

	    connectivity_mapping_bet_b0 -> connectivity_mapping_inverse_AparcAseg;

	    connectivity_mapping_bet_b0 -> connectivity_mapping_track;

	    connectivity_mapping_bet_b0 -> connectivity_mapping_coregister;

	    connectivity_mapping_bet_b0 -> connectivity_mapping_inverse;

	    connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRHlabels;

	    connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRHlabels;

	    connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRHsphere;

	    connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRH;

	    connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRHinflated;

	    connectivity_mapping_fssourceRH -> connectivity_mapping_mris_convertRHwhite;

	    connectivity_mapping_mris_convertRHsphere -> connectivity_mapping_GiftiSurfaces;

	    connectivity_mapping_mris_convertRH -> connectivity_mapping_GiftiSurfaces;

	    connectivity_mapping_mris_convertRHinflated -> connectivity_mapping_GiftiSurfaces;

	    connectivity_mapping_mris_convertRHwhite -> connectivity_mapping_GiftiSurfaces;

	    connectivity_mapping_GiftiSurfaces -> connectivity_mapping_CFFConverter;

	    connectivity_mapping_image2voxel -> connectivity_mapping_dtifit;

	    connectivity_mapping_dtifit -> connectivity_mapping_picopdfs;

	    connectivity_mapping_dtifit -> connectivity_mapping_trace;

	    connectivity_mapping_dtifit -> connectivity_mapping_dteig;

	    connectivity_mapping_dtifit -> connectivity_mapping_fa;

	    connectivity_mapping_trace -> connectivity_mapping_analyzeheader_trace;

	    connectivity_mapping_trace -> connectivity_mapping_trace2nii;

	    connectivity_mapping_analyzeheader_trace -> connectivity_mapping_trace2nii;

	    connectivity_mapping_fa -> connectivity_mapping_analyzeheader_fa;

	    connectivity_mapping_fa -> connectivity_mapping_fa2nii;

	    connectivity_mapping_analyzeheader_fa -> connectivity_mapping_fa2nii;

	    connectivity_mapping_dtlutgen -> connectivity_mapping_picopdfs;

	    connectivity_mapping_picopdfs -> connectivity_mapping_track;

	    connectivity_mapping_track -> connectivity_mapping_camino2trackvis;

	    connectivity_mapping_track -> connectivity_mapping_vtkstreamlines;

	    connectivity_mapping_camino2trackvis -> connectivity_mapping_trk2camino;

	    connectivity_mapping_camino2trackvis -> connectivity_mapping_CreateMatrix;

	    connectivity_mapping_camino2trackvis -> connectivity_mapping_CFFConverter;

	    connectivity_mapping_fssource -> connectivity_mapping_mri_convert_AparcAseg;

	    connectivity_mapping_fssource -> connectivity_mapping_mri_convert_Brain;

	    connectivity_mapping_mri_convert_AparcAseg -> connectivity_mapping_inverse_AparcAseg;

	    connectivity_mapping_mri_convert_AparcAseg -> connectivity_mapping_ROIGen_structspace;

	    connectivity_mapping_ROIGen_structspace -> connectivity_mapping_CreateNodes;

	    connectivity_mapping_CreateNodes -> connectivity_mapping_CreateMatrix;

	    connectivity_mapping_mri_convert_Brain -> connectivity_mapping_NiftiVolumes;

	    connectivity_mapping_mri_convert_Brain -> connectivity_mapping_coregister;

	    connectivity_mapping_mri_convert_Brain -> connectivity_mapping_inverse;

	    connectivity_mapping_coregister -> connectivity_mapping_convertxfm;

	    connectivity_mapping_convertxfm -> connectivity_mapping_inverse_AparcAseg;

	    connectivity_mapping_convertxfm -> connectivity_mapping_inverse;

	    connectivity_mapping_inverse_AparcAseg -> connectivity_mapping_ROIGen;

	    connectivity_mapping_ROIGen -> connectivity_mapping_CreateMatrix;

	    connectivity_mapping_ROIGen -> connectivity_mapping_NiftiVolumes;

	    connectivity_mapping_CreateMatrix -> connectivity_mapping_CFFConverter;

	    connectivity_mapping_CreateMatrix -> connectivity_mapping_FiberDataArrays;

	    connectivity_mapping_CreateMatrix -> connectivity_mapping_FiberDataArrays;

	    connectivity_mapping_CreateMatrix -> connectivity_mapping_FiberDataArrays;

	    connectivity_mapping_CreateMatrix -> connectivity_mapping_FiberDataArrays;

	    connectivity_mapping_FiberDataArrays -> connectivity_mapping_CFFConverter;

	    connectivity_mapping_NiftiVolumes -> connectivity_mapping_CFFConverter;

	    connectivity_mapping_mris_convertRHlabels -> connectivity_mapping_GiftiLabels;

	    connectivity_mapping_GiftiLabels -> connectivity_mapping_CFFConverter;

	  }

	  connectivity_inputnode -> connectivity_mapping_inputnode_within;

	  connectivity_inputnode -> connectivity_mapping_inputnode_within;

	  connectivity_inputnode -> connectivity_mapping_inputnode_within;

	  connectivity_inputnode -> connectivity_mapping_inputnode_within;

	  connectivity_inputnode -> connectivity_mapping_inputnode_within;

	  connectivity_inputnode -> connectivity_mapping_inputnode_within;

	  connectivity_mapping_camino2trackvis -> connectivity_outputnode;

	  connectivity_mapping_CFFConverter -> connectivity_outputnode;

	  connectivity_mapping_CreateMatrix -> connectivity_outputnode;

	  connectivity_mapping_CreateMatrix -> connectivity_outputnode;

	  connectivity_mapping_CreateMatrix -> connectivity_outputnode;

	  connectivity_mapping_fa2nii -> connectivity_outputnode;

	  connectivity_mapping_CreateMatrix -> connectivity_outputnode;

	  connectivity_mapping_ROIGen -> connectivity_outputnode;

	  connectivity_mapping_mri_convert_Brain -> connectivity_outputnode;

	  connectivity_mapping_trace2nii -> connectivity_outputnode;

	  connectivity_mapping_dtifit -> connectivity_outputnode;

	}

