Software#
TRX is integrated into several software libraries:
TRXViz#
TRXViz is a tool for visualization and processing of diffusion-MRI based tractography. Implemented in Rust, it supports fast visualization and basic processing of TRX-based tractography.
pyAFQ#
pyAFQ is a Python library for automated white matter tractography and tractometry. It uses TRX to parallelize and accelerate tractography, as well as to perform batched operations over groups of streamlines in ways that allow handling very large tractograms (>100M streamlines) on standard hardware. See this PR.
Trekker#
Trekker implements parallel transport tractography for generating geometrically smooth streamlines [Aydogan and Shi, 2021]. It uses the TRX C++ implementation for I/O.
DIPY#
DIPY is a library for the analysis of diffusion MRI data [Garyfallidis et al., 2014]. DIPY supports I/O in many different file formats, including TRX. See this PR
QSIPrep & QSIRecon#
QSIPrep is an integrative platform for preprocessing and reconstructing diffusion MRI data [Cieslak et al., 2021]. QSIPrep and its post-processing pipelines, implemented in QSIRecon advance the use of TRX as an interchange format, because they knit together functionality from many different software libraries.
Surfice#
Surfice is a tool for visualizing neuroimaging meshes, tractography streamlines, and connectomes [Rorden, 2025].
SlicerDMRI#
SlicerDMRI is an open source diffusion MRI software, implemented as an extension of 3D Slicer [Norton et al., 2017]. It now supports use of TRX, through its C++ implementation. See this PR.
FSL#
FSL is a comprehensive library of tools for functional MRI, structural MRI, and diffusion MRI analysis. The FSLeyes viewer includes support for TRX as of its 1.20 version release. See this PR.
COMMIT#
COMMIT (Convex Optimization Modeling for Microstructure Informed Tractography) is a framework for microstructure-informed tractography. TRX support in COMMIT using its C++ implementation is currently work-in-progress (see this PR)
brainlife.io#
brainlife.io is a decentralized and open-source cloud platform to support neuroscience research [Hayashi et al., 2024]. It uses TRX for streamline I/O.
Niivue#
Niivue is a WebGL-based visualization library for neuroimaging data, including tractography streamlines. It uses features of TRX to display different groups (e.g., tracts) and their distinct properties. See this PR
DWI2TRX#
The DWI2TRX web application uses WASM-based dcm2niix and niimath as well as WebGPU-based NiiVue, mindgrab and GPUstreamlines to perform a minimal processing pipeline that generates a TRX tractography from NIfTI/bval/bvec files or from a directory of DICOMs. All computations are conducted client-side on the user’s computer, and no data is uploaded to any remote server. It works on any web-enabled device that supports the full WebGPU standard.
Insight ToolKit (ITK)#
ITK is an open-source framework for image analysis. TRX has been integrated as an external module, making it available for users of the ANTS registration framework [Avants et al., 2014]. See this PR.
MRtrix#
MRtrix3 is a fast, flexible and open software framework for medical image processing and visualisation [Tournier et al., 2019]. Integration of TRX support is currently in progress (in this PR).