workflows.dmri.mrtrix.diffusion¶
create_mrtrix_dti_pipeline()¶
Creates a pipeline that does the same diffusion processing as in the dMRI: DTI - MRtrix, FSL example script. Given a diffusion-weighted image, b-values, and b-vectors, the workflow will return the tractography computed from spherical deconvolution and probabilistic streamline tractography
Example¶
>>> dti = create_mrtrix_dti_pipeline("mrtrix_dti")
>>> dti.inputs.inputnode.dwi = 'data.nii'
>>> dti.inputs.inputnode.bvals = 'bvals'
>>> dti.inputs.inputnode.bvecs = 'bvecs'
>>> dti.run()
Inputs:
inputnode.dwi
inputnode.bvecs
inputnode.bvals
Outputs:
outputnode.fa
outputnode.tdi
outputnode.tracts_tck
outputnode.tracts_trk
outputnode.csdeconv
Graph¶
![digraph dtiproc{
label="dtiproc";
dtiproc_inputnode[label="inputnode (utility)"];
dtiproc_bet[label="bet (fsl)"];
dtiproc_MRconvert[label="MRconvert (mrtrix)"];
dtiproc_fsl2mrtrix[label="fsl2mrtrix (mrtrix)"];
dtiproc_dwi2tensor[label="dwi2tensor (mrtrix)"];
dtiproc_tensor2adc[label="tensor2adc (mrtrix)"];
dtiproc_tensor2vector[label="tensor2vector (mrtrix)"];
dtiproc_tensor2fa[label="tensor2fa (mrtrix)"];
dtiproc_gen_WM_mask[label="gen_WM_mask (mrtrix)"];
dtiproc_threshold_wmmask[label="threshold_wmmask (mrtrix)"];
dtiproc_threshold_b0[label="threshold_b0 (mrtrix)"];
dtiproc_median3D[label="median3D (mrtrix)"];
dtiproc_erode_mask_firstpass[label="erode_mask_firstpass (mrtrix)"];
dtiproc_erode_mask_secondpass[label="erode_mask_secondpass (mrtrix)"];
dtiproc_MRmultiply_merge[label="MRmultiply_merge (utility)"];
dtiproc_MRmultiply[label="MRmultiply (mrtrix)"];
dtiproc_threshold_FA[label="threshold_FA (mrtrix)"];
dtiproc_estimateresponse[label="estimateresponse (mrtrix)"];
dtiproc_csdeconv[label="csdeconv (mrtrix)"];
dtiproc_CSDstreamtrack[label="CSDstreamtrack (mrtrix)"];
dtiproc_tracks2prob[label="tracks2prob (mrtrix)"];
dtiproc_tck2trk[label="tck2trk (mrtrix)"];
dtiproc_outputnode[label="outputnode (utility)"];
dtiproc_inputnode -> dtiproc_fsl2mrtrix;
dtiproc_inputnode -> dtiproc_fsl2mrtrix;
dtiproc_inputnode -> dtiproc_bet;
dtiproc_inputnode -> dtiproc_csdeconv;
dtiproc_inputnode -> dtiproc_gen_WM_mask;
dtiproc_inputnode -> dtiproc_tck2trk;
dtiproc_inputnode -> dtiproc_dwi2tensor;
dtiproc_inputnode -> dtiproc_MRconvert;
dtiproc_inputnode -> dtiproc_estimateresponse;
dtiproc_inputnode -> dtiproc_tracks2prob;
dtiproc_bet -> dtiproc_gen_WM_mask;
dtiproc_MRconvert -> dtiproc_threshold_b0;
dtiproc_fsl2mrtrix -> dtiproc_dwi2tensor;
dtiproc_fsl2mrtrix -> dtiproc_csdeconv;
dtiproc_fsl2mrtrix -> dtiproc_estimateresponse;
dtiproc_fsl2mrtrix -> dtiproc_gen_WM_mask;
dtiproc_dwi2tensor -> dtiproc_tensor2adc;
dtiproc_dwi2tensor -> dtiproc_tensor2vector;
dtiproc_dwi2tensor -> dtiproc_tensor2fa;
dtiproc_tensor2fa -> dtiproc_MRmultiply_merge;
dtiproc_tensor2fa -> dtiproc_outputnode;
dtiproc_gen_WM_mask -> dtiproc_csdeconv;
dtiproc_gen_WM_mask -> dtiproc_threshold_wmmask;
dtiproc_threshold_wmmask -> dtiproc_CSDstreamtrack;
dtiproc_threshold_b0 -> dtiproc_median3D;
dtiproc_median3D -> dtiproc_erode_mask_firstpass;
dtiproc_erode_mask_firstpass -> dtiproc_erode_mask_secondpass;
dtiproc_erode_mask_secondpass -> dtiproc_MRmultiply_merge;
dtiproc_MRmultiply_merge -> dtiproc_MRmultiply;
dtiproc_MRmultiply -> dtiproc_threshold_FA;
dtiproc_threshold_FA -> dtiproc_estimateresponse;
dtiproc_estimateresponse -> dtiproc_csdeconv;
dtiproc_csdeconv -> dtiproc_CSDstreamtrack;
dtiproc_csdeconv -> dtiproc_outputnode;
dtiproc_CSDstreamtrack -> dtiproc_outputnode;
dtiproc_CSDstreamtrack -> dtiproc_tracks2prob;
dtiproc_CSDstreamtrack -> dtiproc_tck2trk;
dtiproc_tracks2prob -> dtiproc_outputnode;
dtiproc_tck2trk -> dtiproc_outputnode;
}](../../_images/graphviz-ef2b95bafd3476fd154f681f71e8b34085025e16.png)