Heuristic neighbourhood tractography is defunct. All hnt- experiment scripts have been removed, along with the underlying functions. This approach has been deprecated since 2017, and has no remaining advantages compared to probabilistic neighbourhood tractography. There is new interoperability with MRtrix3, including read support for the mif image format and tck tractography format. These files can now be used as input to scripts like image, trkinfo and graph-build. TractoR's tractography functions have been substantially refactored for better generality, partly to accommodate MRtrix tck files as input. As a result it is no longer necessary for streamlines to be written to file before being further used – they can be generated and processed entirely in memory. MRtrix-format tck tractography files can be converted to TrackVis trk format using the new tck2trk script. The MRtrix viewer, MRView, is now available as an external viewer through the view script. The new compare script compares image values to check whether two images contain the same data. A history of the TractoR scripts used to generate a given image is now stored in the commandHistory tag, and merged with the equivalent from MRtrix where relevant. True RGB NIfTI files are now supported for reading and writing, and internal methods for the tensorfit script will now produce an RGB colour fractional anisotropy map. RGB images cannot yet be transformed between spaces, though. A colour fractional anisotropy map is now additionally produced by the internal diffusion tensor fitting code. Complex-valued images are also now supported internally. When interpreting file paths, furrow will now leave any that are explicitly given (without requiring an extension to be added) as they are. This is partly because trk and tck files with the same base name can currently coexist. It is now possible for more object types to be summarised by peek. Workflow prerequisites are now checked more carefully. The apply script is now much more memory-efficient when combining many images. Functions from tractor.base that were deprecated in the 3.0.0 release have now been removed.

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