4. New or renamed commands
5ttgen hsvs
New algorithm for generating a 5TT image for ACT. Takes as input a FreeSurfer output, but unlike 5ttgen freesurfer, utilises the surface-based cortical estimates rather than only the aseg image. Cleaner 5TT images than 5ttgen fsl, but not guaranteed to work in all scenarios. Feedback welcome. (Thanks for collaboration @Antonin_Skoch and @cbajada)
connectomeedit
Performs basic operations on connectome matrix numerical data.
dwicat
In addition to concatenating multiple DWI series (which could otherwise be done using mrcat), also accounts for unwanted variations in image intensities across series, by estimating the multiplicative factors required to make the b=0 images in each series of comparable intensity. Intended for platforms whereby multi-shell acquisition is only possible by running multiple protocols, and thus there may re-calibration in any stage of the acquisition & reconstruction process.
dwifslpreproc
dwipreproc has been renamed to dwifslpreproc. This provides greater attribution for the FSL commands principally responsible for performing the image pre-processing, and will reduce likelihood of naming conflicts with future MRtrix3 additions.
dwinormalise
The result of refactoring:
-
dwinormaliseis now a Python script rather than a C++ compiled binary. -
dwinormalise individualduplicates the functionality of former binarydwinormalise. -
dwinormalise groupduplicates the functionality of former Python scriptdwiintensitynorm.
fixelconnectivity
Generate a fixel-fixel connectivity matrix and write to filesystem. Fixel-fixel connectivity matrix generation is ~ 4-5 times faster and requires ~ 4-5 times less RAM than it did in previous software versions where this step was performed within the fixelcfestats command. This is an essential step for the FBA pipeline. Matrix data are written to the filesystem using a new format.
fixelfilter
Perform filtering operations on fixel data. This includes smoothing, and a preliminary connected-component algorithm. Can operate on individual fixel data files, or all data files within a fixel format directory. Duplicates functionality that previously occurred within the fixelcfestats command (and is therefore a crucial component of the FBA pipeline).
for_each
Renamed from foreach due to the latter being a reserved keyword in zsh, which will be usurping bash as the default on MacOS.
labelstats
Provides statistics on label images (i.e. parcellations): centres of mass and voxel counts.
mrcentroid
Outputs the centre of mass / centre of gravity of an image.
mrcolour
Applies a colour map to an image; particularly useful in conjunction with the PNG image format for exporting quantitative image data to images at their native resolution with stringent intensity / colour mapping control.
mrgrid
mrgrid is a replacement to mrcrop, mrpad and mrresize.
mrtrix_cleanup
Searches for and deletes MRtrix3 piped images and Python script scratch directories.
responsemean
Replacement for former bash script average_response. Default mechanism for response function averaging is slightly different to that of average_response, but in most cases results should be almost identical.