Releases: tractor/tractor
Releases · tractor/tractor
TractoR version 3.4.3
- Dependency packages
jsonlite
,yaml
,Rcpp
andRNifti
have been updated for compatibility with the now-released R 4.4.0.
TractoR version 3.4.2
- Package unit tests have been moved from the
testthat
to thetinytest
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 andigraph
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 This was already the case, but the documentation was out of date.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.
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 bytractor
,plough
andfurrow
, if it is set, andfurrow
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.
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 andtck
tractography format. These files can now be used as input to scripts likeimage
,trkinfo
andgraph-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 TrackVistrk
format using the newtck2trk
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 becausetrk
andtck
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.
TractoR version 3.3.5
- The eddy workflow now adds the argument
--data_is_shelled
when calling theeddy
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 fromeddy
which is often spurious. - The
dpreproc
script now also checks for theeddy_openmp
variant executable name before deciding not to run eddy. - A mistake in the self-documentation of the
workflow
script has been corrected.
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).
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.
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.