MRtrix 0.2 equivalent commands

For those users moving to MRtrix3 from the old MRtrix 0.2.x software, this list provides the equivalent command names for the functionalities that they are accustomed to from the older version of the software. The new command naming scheme was carefully designed, so we hope people agree that it makes sense, and allows users to easily find the command functionalities available that are relevant for the data they are processing.

Further information can be found on these commands either through the documentation, or by typing the binary name at the command-line with no arguments to access the help file for that command.

MRtrix 0.2.x

MRtrix3

Comments

average

mrmath

Use mean statistic as second argument, and -axis option

cat_tracks

tckedit

Simply provide multiple input track files to the command

cleanup_ANTS_warp

no equivalent

csdeconv

dwi2fod

dicom_filename

no equivalent

See dcminfo

dir2amp

peaks2amp

disp_profile

shview

dwi2SH

amp2sh

dwi2tensor

dwi2tensor

erode

maskfilter

Specify erode or dilate algorithm as second argument

estimate_response

dwi2response manual

The dwi2response script also has a number of algorithms for automatically selecting single-fibre voxels in order to estimate the response function; see the relevant help page

filter_tracks

tckedit

find_SH_peaks

sh2peaks

gen_ROI

no equivalent

gen_WM_mask

no equivalent

Use of this command was discouraged and so it has been discontinued

gen_unit_warp

warpinit

gendir

dirgen

The electrostatic repulsion algorithm now only uses an exponent of 2 by default, rather than increasing in power over iterations; this was found to give poorer minimum-angle values, but superior conditioning of direction schemes

import_tracks

tckconvert

median3D

mrfilter

Specify median algorithm as second argument

mrabs

mrcalc

Use -abs operator

mradd

mrcalc or mrmath

E.g. mrcalc A.mif B.mif -add out.mif or mrmath A.mif B.mif sum out.mif

mrcat

mrcat

mrconvert

mrconvert

mrinfo

mrinfo

mrmult

mrcalc or mrmath

E.g. mrcalc A.mif B.mif -mult out.mif or mrmath A.mif B.mif product out.mif

mrstats

mrstats

mrtransform

mrtransform

mrview

mrview

normalise_tracks

tcktransform

read_dicom

dcminfo

read_ximg

no equivalent

resample_tracks

tcksample

sample_tracks

tcksample

sdeconv

dwi2fod

select_tracks

tckedit

streamtrack

tckgen

tensor2ADC

tensor2metric

Use -adc output option

tensor2FA

tensor2metric

Use -fa output option

tensor2vector

tensor2metric

Use -vector output option

tensor_metric

tensor2metric

threshold

mrthreshold

Note that automatic threshold parameter determination (i.e. if you don’t explicitly provide an option to specify how the thresholding should be performed) is done using a different heuristic to that in the MRtrix 0.2 command

track_info

tckinfo

tracks2prob

tckmap

tracks2vtk

tckconvert

truncate_tracks

tckedit