Published October 13, 2025 | Version v3.5.0
Software Open

TractoR

Creators

  • 1. University College London
  • 2. The University of Edinburgh

Description

  • TractoR now requires R v3.6.2 (from 2019) or later.
  • MRtrix interoperability now extends to session directories. There is support for managed constrained spherical deconvolution file locations within an mrtrix subdirectory.
  • There is a new csd script for running MRtrix CSD through TractoR, and workflows for key commands dwi2response and dwi2fod.
  • Registration transformations are now preferentially stored in flat .Rdata files again. These are easier to handle and can now encapsulate all necessary metadata, including for nonlinear warps. The .xfmb folder format can still be read.
  • The test dataset stored at tests/data/session has been rebuilt using current software, and therefore differs in various (mostly small) ways from previous releases.
  • A new reg-reverse script creates a transformation that is the logical inverse of an existing one.
  • The new gradsample script can be used to subsample diffusion MRI acquisitions.
  • The import script can now import multiple diffusion or functional data volumes, which will be merged together in order.
  • The gradread script is now more flexible with its output, and can create standalone gradient files in addition to working with sessions.
  • Handling of groups of related files on disk is now more consistent and unified. Mapping is now supported for images outside of session hierarchies, and favoured over symbolic linking for better portability across operating systems and on cloud-backed and remote filesystems. Remaining uses of symlinking are mostly for compatibility with other software.
  • The furrow command is now written in pure R, rather than being a shell script, and is run through the littler frontend. This should make the command less fragile in its interface to R, notably when handling paths containing spaces, and similar treatment is planned for tractor and plough in a future release. The small first-party package arrg is now bundled to support this interface.
  • Experiment scripts can now be bundled with arbitrary R packages and found by TractoR via the TRACTOR_PACKAGES environment variable.
  • The plough command gains a -I flag to allow values to be passed into the command through a pipe.
  • TractoR now provides a simple Rprofile that can be sourced from the user's equivalent startup file to provide ready access to TractoR's packages and environment in R sessions.
  • The graph-decompose script now has a mode to decompose a graph into connected components.
  • The slice script gains a Volume option to specify a required volume if the input is 4D.
  • Output from the list script has been improved, and a new Descriptions:true option incorporates the start of the script's self-description into the summary. Groupings are no longer hard-coded in this script, but determined by a comment in each script.
  • Unnamed arguments may now be passed to a workflow via the workflow script.
  • Long-deprecated config variables in the view, pnt-data and bedpost scripts have now been removed.
  • The global Arguments vector seen by TractoR scripts is now named, using arguments to requireArguments(), for ease of later reference.
  • The internals of the tractography code have been tweaked to try to avoid sporadic segmentation faults on some platforms.

Notes

If you use this software, please cite it using the metadata from this file.

Files

tractor/tractor-v3.5.0.zip

Files (66.7 MB)

Name Size Download all
md5:cc2e14c8f86694c36f11c2286904e83d
66.7 MB Preview Download

Additional details

Related works

Is supplement to
Software: https://github.com/tractor/tractor/tree/v3.5.0 (URL)

Software

Repository URL
https://github.com/tractor/tractor