Full changelog

Bug fixes

• tckglobal: Fix operation following changes made as part of DWI metadata fixes for master #3011 resulting in multiple attempts to construct an Image class from the same input header. Fixes tckglobal: don't invoke get_image() with invalid Header! #3171.

  Also fix several race conditions identified using thread sanitiser.

• Fix race condition in ThreadedLoop. Issue identified by thread sanitizer while working on tckglobal: Fix operation #3172.

• tcksift2: Minor fixes to diagnosis data: the current DWI::Fixel_map<> class (to be deprecated in the future) contains at index 0 a fixel with an empty constructor. Any diagnosis information presented to the user should therefore be computed without consideration for this non-existing fixel. Reported by @ppruc.

• fsl.check_first(): Handle run_first_all providing no HOLDID: follows fsl.check_first(): Second attempt at refinement #2609. Hopefully addresses issue reported on forum.

• MR::Axes::permutations_type: Fix is_identity().

• Fix phase encoding handling on 3.0.7. Fixes dwifslpreproc: mrinfo -export_pe_eddy with mif files #3142.

• mrmath: Typo in error message

MRView

• mrview: Bugfix in rendering of cubes in connectome tool: problem introduced in 92eee2a as part of Connectome tool #283.

• Fix tractography rendering performance on macOS: this PR fixes the longstanding performance issues in the viewer on macOS when visualising tractography streamlines (using pseudotubes).

• Fix ROI edits disappearing on MacOS: this small change fixes mrview: ROI edits deleted after two elements drawn #2319.

Documentation

• Docs: Description of options with single-shell data: replacement of Docs: Describe use of MSMT with single-shell data #2441, targeting master.

• Stats commands: Clarify non-stationarity correction in help pages.

• tcksift2 & afdconnectivity: Update citation.

• tck2connectome: Add default assignment mechanism to docs, as requested on forum.

Enhancements

• DICOM: Performance fix to wildcard matching.

• mesh2voxel: Accept >3D image as template voxel grid: simple change to reduce the template voxel grid image to 3D if the image provided by the user is > 3D.

• Pipe image format: Revise error message.

Build-related issues

• Update configure script for Xcode26 compatibility: link against OpenGL only, not AGL as it is no longer included in MacOS Tahoe/Xcode26 (https://bugreports.qt.io/browse/QTBUG-137687).

• Fix Eigen 3.4.1 type mismatch in ColourMap clamping: fix compilation error leading to Eigen::internal::traits<double> errors.

• mrcalc: Docs: Combining mag&phase into complex data: caught myself feeling the need to demonstrate this to a colleague and realised that it really should be an example usage.

• Testing: Relax tolerances on fixelcfestats tests: tests were observed to fail on MacOS in Fix phase encoding handling on 3.0.7 #3146.