workflows.dmri.camino.diffusion¶
create_camino_dti_pipeline()¶
Creates a pipeline that does the same diffusion processing as in the dMRI: Camino, DTI 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
>>> nipype_camino_dti = 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 (utility)"];
dtiproc_outputnode[label="outputnode (utility)"];
subgraph cluster_dtiproc_tractography {
label="tractography";
dtiproc_tractography_inputnode1[label="inputnode1 (utility)"];
dtiproc_tractography_image2voxel[label="image2voxel (camino)"];
dtiproc_tractography_bet[label="bet (fsl)"];
dtiproc_tractography_fsl2scheme[label="fsl2scheme (camino)"];
dtiproc_tractography_dtlutgen[label="dtlutgen (camino)"];
dtiproc_tractography_dtifit[label="dtifit (camino)"];
dtiproc_tractography_trackdt[label="trackdt (camino)"];
dtiproc_tractography_cam2trk_dt[label="cam2trk_dt (camino2trackvis)"];
dtiproc_tractography_trace[label="trace (camino)"];
dtiproc_tractography_analyzeheader_trace[label="analyzeheader_trace (camino)"];
dtiproc_tractography_trace2nii[label="trace2nii (misc)"];
dtiproc_tractography_fa[label="fa (camino)"];
dtiproc_tractography_analyzeheader_fa[label="analyzeheader_fa (camino)"];
dtiproc_tractography_fa2nii[label="fa2nii (misc)"];
dtiproc_tractography_dteig[label="dteig (camino)"];
dtiproc_tractography_picopdfs[label="picopdfs (camino)"];
dtiproc_tractography_trackpico[label="trackpico (camino)"];
dtiproc_tractography_cam2trk_pico[label="cam2trk_pico (camino2trackvis)"];
dtiproc_tractography_inputnode1 -> dtiproc_tractography_cam2trk_pico;
dtiproc_tractography_inputnode1 -> dtiproc_tractography_cam2trk_pico;
dtiproc_tractography_inputnode1 -> dtiproc_tractography_fsl2scheme;
dtiproc_tractography_inputnode1 -> dtiproc_tractography_fsl2scheme;
dtiproc_tractography_inputnode1 -> dtiproc_tractography_bet;
dtiproc_tractography_inputnode1 -> dtiproc_tractography_cam2trk_dt;
dtiproc_tractography_inputnode1 -> dtiproc_tractography_cam2trk_dt;
dtiproc_tractography_inputnode1 -> dtiproc_tractography_trace2nii;
dtiproc_tractography_inputnode1 -> dtiproc_tractography_analyzeheader_fa;
dtiproc_tractography_inputnode1 -> dtiproc_tractography_analyzeheader_fa;
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_image2voxel;
dtiproc_tractography_image2voxel -> dtiproc_tractography_dtifit;
dtiproc_tractography_bet -> dtiproc_tractography_trackdt;
dtiproc_tractography_bet -> dtiproc_tractography_trackpico;
dtiproc_tractography_fsl2scheme -> dtiproc_tractography_dtifit;
dtiproc_tractography_fsl2scheme -> dtiproc_tractography_dtlutgen;
dtiproc_tractography_dtlutgen -> dtiproc_tractography_picopdfs;
dtiproc_tractography_dtifit -> dtiproc_tractography_trackdt;
dtiproc_tractography_dtifit -> dtiproc_tractography_trace;
dtiproc_tractography_dtifit -> dtiproc_tractography_fa;
dtiproc_tractography_dtifit -> dtiproc_tractography_dteig;
dtiproc_tractography_dtifit -> dtiproc_tractography_picopdfs;
dtiproc_tractography_trackdt -> dtiproc_tractography_cam2trk_dt;
dtiproc_tractography_trace -> dtiproc_tractography_analyzeheader_trace;
dtiproc_tractography_trace -> dtiproc_tractography_trace2nii;
dtiproc_tractography_analyzeheader_trace -> dtiproc_tractography_trace2nii;
dtiproc_tractography_fa -> dtiproc_tractography_analyzeheader_fa;
dtiproc_tractography_fa -> dtiproc_tractography_fa2nii;
dtiproc_tractography_analyzeheader_fa -> dtiproc_tractography_fa2nii;
dtiproc_tractography_picopdfs -> dtiproc_tractography_trackpico;
dtiproc_tractography_trackpico -> dtiproc_tractography_cam2trk_pico;
}
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;
}](../../_images/graphviz-8f3b7c8edf6f650b0a73d034f7ab2dabb039c1d8.png)