Reconstruct DTI from DWI using mrtrix

ANTs lacks dcm to dwi to dti functionality. We previously relied on camino but this software is no longer maintained, afaik. thus mrtrix.

brief notes on how to go from dicom to nifti files we can use in ants.

useful programs

mrconvert sid/ep2d_64dir/date/ptid /tmp/my.mif                                # convert dcm to mif

dwidenoise /tmp/my.mif /tmp/myd.mif                                           # mysterious denoising method for dwi

dwiextract /tmp/myd.mif - -bzero | mrmath - mean /tmp/mymeanb0.nii.gz -axis 3 # mean b0 image

dwipreproc -rpe_none /tmp/my.mif /tmp/myp.mif                                 # preprocess dwi e.g. with motion (needs fsl)

dwi2mask /tmp/myd.mif /tmp/mymask.nii.gz                                      # mask dwi (not reliably)

dwi2tensor /tmp/myd.mif /tmp/mydti.nii.gz                                     # convert to dti

tensor2metric -fa /tmp/myfa.nii.gz /tmp/mydti.nii.gz                          # get fa from dti

one might also do warping with ANTs or other programs

i would like to know how to apply motion correction ...