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nipype.workflows.camino.diffusion

create_camino_dti_pipeline()

Creates a pipeline that does the same diffusion processing as in the camino_dti_tutorial example script. Given a diffusion-weighted image, b-values, and b-vectors, the workflow will return the tractography computed from diffusion tensors and from PICo probabilistic tractography.

Example

>>> import os
>>> import nipype.workflows.camino as cmonwk
>>> nipype_camino_dti = cmonwk.diffusion.create_camino_dti_pipeline("nipype_camino_dti")
>>> nipype_camino_dti.inputs.inputnode.dwi = os.path.abspath('dwi.nii')
>>> nipype_camino_dti.inputs.inputnode.bvecs = os.path.abspath('bvecs')
>>> nipype_camino_dti.inputs.inputnode.bvals = os.path.abspath('bvals')
>>> nipype_camino_dti.run()                  

Inputs:

inputnode.dwi
inputnode.bvecs
inputnode.bvals

Outputs:

outputnode.fa
outputnode.trace
outputnode.tracts_pico
outputnode.tracts_dt
outputnode.tensors

Graph

digraph dtiproc{

  label="dtiproc";

  dtiproc_inputnode[label="inputnode.IdentityInterface.utility"];

  dtiproc_outputnode[label="outputnode.IdentityInterface.utility"];

  subgraph cluster_dtiproc_tractography {

      label="tractography";

    dtiproc_tractography_inputnode1[label="inputnode1.IdentityInterface.utility"];

    dtiproc_tractography_bet[label="bet.BET.fsl"];

    dtiproc_tractography_image2voxel[label="image2voxel.Image2Voxel.camino"];

    dtiproc_tractography_fsl2scheme[label="fsl2scheme.FSL2Scheme.camino"];

    dtiproc_tractography_dtifit[label="dtifit.DTIFit.camino"];

    dtiproc_tractography_fa[label="fa.ComputeFractionalAnisotropy.camino"];

    dtiproc_tractography_analyzeheader_fa[label="analyzeheader_fa.AnalyzeHeader.camino"];

    dtiproc_tractography_fa2nii[label="fa2nii.CreateNifti.misc"];

    dtiproc_tractography_dteig[label="dteig.ComputeEigensystem.camino"];

    dtiproc_tractography_dtlutgen[label="dtlutgen.DTLUTGen.camino"];

    dtiproc_tractography_picopdfs[label="picopdfs.PicoPDFs.camino"];

    dtiproc_tractography_trackpico[label="trackpico.TrackPICo.camino"];

    dtiproc_tractography_cam2trk_pico[label="cam2trk_pico.Camino2Trackvis.camino2trackvis"];

    dtiproc_tractography_trace[label="trace.ComputeTensorTrace.camino"];

    dtiproc_tractography_analyzeheader_trace[label="analyzeheader_trace.AnalyzeHeader.camino"];

    dtiproc_tractography_trace2nii[label="trace2nii.CreateNifti.misc"];

    dtiproc_tractography_trackdt[label="trackdt.TrackDT.camino"];

    dtiproc_tractography_cam2trk_dt[label="cam2trk_dt.Camino2Trackvis.camino2trackvis"];

    dtiproc_tractography_inputnode1 -> dtiproc_tractography_analyzeheader_fa;

    dtiproc_tractography_inputnode1 -> dtiproc_tractography_analyzeheader_fa;

    dtiproc_tractography_inputnode1 -> dtiproc_tractography_cam2trk_pico;

    dtiproc_tractography_inputnode1 -> dtiproc_tractography_cam2trk_pico;

    dtiproc_tractography_inputnode1 -> dtiproc_tractography_cam2trk_dt;

    dtiproc_tractography_inputnode1 -> dtiproc_tractography_cam2trk_dt;

    dtiproc_tractography_inputnode1 -> dtiproc_tractography_analyzeheader_trace;

    dtiproc_tractography_inputnode1 -> dtiproc_tractography_analyzeheader_trace;

    dtiproc_tractography_inputnode1 -> dtiproc_tractography_fa2nii;

    dtiproc_tractography_inputnode1 -> dtiproc_tractography_trace2nii;

    dtiproc_tractography_inputnode1 -> dtiproc_tractography_fsl2scheme;

    dtiproc_tractography_inputnode1 -> dtiproc_tractography_fsl2scheme;

    dtiproc_tractography_inputnode1 -> dtiproc_tractography_bet;

    dtiproc_tractography_inputnode1 -> dtiproc_tractography_image2voxel;

    dtiproc_tractography_bet -> dtiproc_tractography_trackpico;

    dtiproc_tractography_bet -> dtiproc_tractography_trackdt;

    dtiproc_tractography_image2voxel -> dtiproc_tractography_dtifit;

    dtiproc_tractography_fsl2scheme -> dtiproc_tractography_dtifit;

    dtiproc_tractography_fsl2scheme -> dtiproc_tractography_dtlutgen;

    dtiproc_tractography_dtifit -> dtiproc_tractography_trace;

    dtiproc_tractography_dtifit -> dtiproc_tractography_fa;

    dtiproc_tractography_dtifit -> dtiproc_tractography_dteig;

    dtiproc_tractography_dtifit -> dtiproc_tractography_trackdt;

    dtiproc_tractography_dtifit -> dtiproc_tractography_picopdfs;

    dtiproc_tractography_fa -> dtiproc_tractography_analyzeheader_fa;

    dtiproc_tractography_fa -> dtiproc_tractography_fa2nii;

    dtiproc_tractography_analyzeheader_fa -> dtiproc_tractography_fa2nii;

    dtiproc_tractography_dtlutgen -> dtiproc_tractography_picopdfs;

    dtiproc_tractography_picopdfs -> dtiproc_tractography_trackpico;

    dtiproc_tractography_trackpico -> dtiproc_tractography_cam2trk_pico;

    dtiproc_tractography_trace -> dtiproc_tractography_analyzeheader_trace;

    dtiproc_tractography_trace -> dtiproc_tractography_trace2nii;

    dtiproc_tractography_analyzeheader_trace -> dtiproc_tractography_trace2nii;

    dtiproc_tractography_trackdt -> dtiproc_tractography_cam2trk_dt;

  }

  dtiproc_tractography_cam2trk_dt -> dtiproc_outputnode;

  dtiproc_tractography_cam2trk_pico -> dtiproc_outputnode;

  dtiproc_tractography_fa2nii -> dtiproc_outputnode;

  dtiproc_tractography_trace2nii -> dtiproc_outputnode;

  dtiproc_tractography_dtifit -> dtiproc_outputnode;

  dtiproc_inputnode -> dtiproc_tractography_inputnode1;

  dtiproc_inputnode -> dtiproc_tractography_inputnode1;

  dtiproc_inputnode -> dtiproc_tractography_inputnode1;

}