List of MRtrix3 scripts

Command Synopsis
5ttgen Generate a 5TT image suitable for ACT
dwi2response Estimate response function(s) for spherical deconvolution
dwibiascorrect Perform B1 field inhomogeneity correction for a DWI volume series
dwigradcheck Check the orientation of the diffusion gradient table
dwiintensitynorm Performs a global DWI intensity normalisation on a group of subjects using the median b=0 white matter value as the reference
dwipreproc Perform diffusion image pre-processing using FSL’s eddy tool; including inhomogeneity distortion correction using FSL’s topup tool if possible
labelsgmfix In a FreeSurfer parcellation image, replace the sub-cortical grey matter structure delineations using FSL FIRST
population_template Generates an unbiased group-average template from a series of images