tractor.base - TractoR version 3.4.5

The required RNiftyReg could fail to install on some platforms. This has now been corrected, and other bug-fixes to the package back-ported.

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Published by jonclayden 11 months ago

tractor.base - TractoR version 3.4.4

• Auxiliary binaries from the bin/exec and bin/extra subdirectories have been moved to libexec to help with packaging TractoR for Homebrew according to its expectations.

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Published by jonclayden over 1 year ago

tractor.base - TractoR version 3.4.3

• Dependency packages jsonlite, yaml, Rcpp and RNifti have been updated for compatibility with the now-released R 4.4.0.

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Published by jonclayden almost 2 years ago

tractor.base - TractoR version 3.4.2

• Package unit tests have been moved from the testthat to the tinytest framework.
• Several tweaks have been made to improve compatibility with R 4.3.x and the upcoming R 4.4.0, as well as divest 1.0 and igraph 2.0.
• The minimum required version of R has been updated in the documentation to 3.5.0. This was already the case, but the documentation was out of date. TractoR's continuous integration tests now also run on old versions of R to help ensure the minimum version specified is accurate.
• Two spurious errors that could arise during an interactive run of the dpreproc script have been corrected.

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Published by jonclayden almost 2 years ago

tractor.base - TractoR version 3.4.1

• Several tweaks have been made to better support paths containing spaces, particularly for session paths in workflows. In support of this, two small new features have been added: the new TRACTOR_WORKING_DIR environment variable is now used as a default working directory by tractor, plough and furrow, if it is set, and furrow gains a -r flag to request relative paths be substituted rather than absolute ones. This is used in certain workflows to work around third-party tools' own difficulties with paths containing spaces.
• When writing an image to file, any existing "tags" file with the corresponding name is now always overwritten, to avoid the auxiliary file getting out of sync with the image file.
• Relative paths should now be correct when the reference path is a directory.
• The working directory should no longer be erroneously prepended to image paths beginning with a tilde (~), which indicates a home directory on Unix-like systems.
• The bids script would sometimes attempt to copy an image file with no extension, leading to an error. This has been corrected.
• Decomposition applied to a transformation object containing only one transform now works as expected.

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Published by jonclayden over 2 years ago

tractor.base - TractoR version 3.4.0

• 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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Published by jonclayden almost 3 years ago

tractor.base - TractoR version 3.3.5

• The eddy workflow now adds the argument --data_is_shelled when calling the eddy executable, since the absence of this flag frequently caused confusion among users. This has no effect on the output from the workflow, except to silence an error from eddy which is often spurious.
• The dpreproc script now also checks for the eddy_openmp variant executable name before deciding not to run eddy.
• A mistake in the self-documentation of the workflow script has been corrected.

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Published by jonclayden almost 5 years ago

tractor.base - TractoR version 3.3.4

• Small tweaks have been made for better compatibility with the Apple ARM64 platform (M1 chip). This is also the first release available through Homebrew for ARM64.
• Paths to images represented using the Windows Universal Naming Convention (e.g. \\server\dir\image.nii.gz) are now supported (issue #5).
• Offline documentation no longer contains Google Analytics code (issue #4).

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Published by jonclayden about 5 years ago

tractor.base - TractoR version 3.3.3

• Small corrections have been made for compatibility with R v4.0.0, which was recently released.
• The interface for selecting a T2-weighted reference volume in the dpreproc script mixed up volume indices in the original dataset and the low b-value subset, which could lead to spurious errors. This has been corrected.
• The graph-viz script should no longer ask repeatedly about copying the figure to a PDF file.
• Empty graphs are now summarised a little more clearly.

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Published by jonclayden about 5 years ago

tractor.base - TractoR version 2.5.2

The current version of TractoR as of 20th May 2014. For a historical changelog please see http://www.tractor-mri.org.uk/changelog.

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Published by jonclayden almost 12 years ago