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