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FSL 6.0.7.4, 29th September 2023

fmrib-unpack 3.7.0 -> 3.7.1

  • MNT: Don't crash if fillVisits(mode) is applied to empty data

  • Don't crash if fillVisits(mode) is applied to empty data, and don't crash on invalid expressions.

  • Fix logic error handling the --no_download flag.

  • Migrate from setup.py to pyproject.toml.

  • MNT: Administrative and documentation updates

Most notably, a brief example on merging two data sets together using a UKB bridging file

Detailed history

  • MNT: Don't crash if fillVisits(mode) is applied to empty data, and don't crash on invalid expressions
  • TEST: ignore logger
  • MNT: Replace setup.py with pyproject.toml. Add nbclassic to dependencies for demo notebook
  • MNT: Use nbclassic instead of notebook
  • BF: Wrong logic
  • DOC: Changelog
  • CI: Clean up pipeline logic
  • BF: Bug in pyproject
  • TEST: import nbclassic, server mgmt functions have been moved to jupyter_server
  • CI: No longer have requirements files
  • CI: No longer have requirements files
  • DOC: Example on using bridge file to merge two data sets
  • MNT: generate demo notebook, bump version
  • MNT: version
  • MNT: Update internal copies of UKB schema files
  • MNT: only pass infer_datetime_format in old pandas versions
  • MNT: Regenerate notebooks
  • MNT: Missing demo data file
  • MNT: Re-generate notebooks again

fsleyes 1.8.3 -> 1.9.0

  • ENH: Keyboard shortcut to toggle all but first/bottom overlay

New keyboard shortcut (control+shift+f) to toggle visibility of all overlays except for the first/bottom one, by Christopher G. Schwarz (@CGSchwarzMayo) (!406, GitHub PR.

  • Add 'fslview' displaySpace, and change orientation warnings behavior

Contributed by Christopher G. Shwarz (Github PR)

  • New fslview displaySpace setting uses pixdim-flip, similar to fslview/fsl coordinate space behavior
  • Orientation labels are now displayed in all scenarios, except when displaySpace is set to 'scaledVoxel'

  • The location panel orientation warning may be suppressed with a new --hideOrientationWarnings command-line flag

  • MNT: Attempt to find reference images for freesurfer/gifti meshes.

FreeSurfer stores undocumented metadata in generated GIfTI files (e.g. from mris_convert lh.pial lh.surf.gii); these files also frequently contain vertices defined in the FreeSurfer coordinate system rather than a RAS coordinate system, and so need to be transformed accordingly. This MR detects such files, and initialises the .MeshOpts.coordSpace setting to 'torig' so that the surface should correctly align with its reference image. More information on this can be found at:

  • https://neurostars.org/t/transform-freesurfer-mesh-coordinates-to-volume-coordinates/23693/10

  • https://github.com/nipy/nibabel/discussions/1249

  • MNT: Update for compatibility with matplotlib 3.8

It is no longer possible to give a colourmap a name which is different from the key under which it is registered. So fsleyes colour maps with names the same as built-ins are now registered as "fsleyes_{cmap}". The relevant matplotlib change is https://github.com/matplotlib/matplotlib/pull/25479

Detailed history

  • Add ctrl+shift+f hotkey: toggle all overlays > 1
  • STY: Minor formatting
  • DOC: Changelog, userdocs
  • Add 'fslview' displaySpace, and change orientation warnings behavior * fslview-compatible displaySpace uses pixdim-flip, similar to fslview/fsl coordinate space behavior * Orientation labels are now displayed when in pixdim (scaledVoxels) or pixdim-flip (fslview) spaces, but a warning is displayed that they may be incorrect. * This warning may be suppressed with a new --hideOrientationWarnings
  • RF: Invert logic to avoid double negative - setting is now showOrientationWarning. Command-line option is still --hideOrientationWarning though. Changed short form to -how from -now
  • RF: "fslview-compatible" -> "FSLView mode"
  • RF: Simply orientation label logic - show data labels only when display space is 'scaledVoxel', and show L/R/etc labels in all other situations
  • RF: Schedule canvas redraws on idle loop to reduce unneceesary redraws
  • RF: No need for another warning message
  • MNT: Make sure canvas refreshes when labels change
  • DOC: Note on FSLView mode, changelog, some troubleshooting comments on wxpython/GLX
  • TEST: Unit tests for fslview mode
  • MNT: Mention fslview mode in API docs
  • MNT: Print message in scaledVoxel shell functions
  • DOC: Another note on FSLView mode
  • TEST: Don't hang tests via error dialog
  • DOC: API note about how all bets are off when setting NiftiOpts.transform directly
  • MNT: Adjust display space warning
  • CI: default branch changed to main
  • MNT: Update for compatibility with matplotlib 3.8 - it is no longer possible to give a colourmap a name which is different from the key under which it is registered. So fsleyes colour maps with names the same as built-ins are now registered as "fsleyes_{cmap}".
  • MNT: Need latest props
  • DOC: Changelog
  • CI: Change dev install regime, as pip install --pre seems to ignore dev packages installed from git repos or tarballs
  • TEST: expected cmap names now prefixed
  • MNT: Attempt to find reference images for freesurfer/gifti meshes. Try to detect freesurfer-generated giftis, and set coordSpace accordingly.
  • TEST: Test find*Image functions
  • MNT: Update minimum fslpy version
  • DOC: Changelog
  • MNT: String formatting
  • BF: Make sure Action.destroy is called on tool menu items
  • RF: Ability to set a file option (e.g. mesh --refImage) to "None"
  • TEST: Update benchmark - mesh reference is now set for surface/nifti loaded from same directory. This is affecting the lightbox slice spacing in this particular test.
  • RF: Account for small possibility of atexit handler being called just before nbproc.communicate
  • TEST: Colliding cmaps now prefixed with 'fsleyes_'
  • MNT: More detailed comment about nibabel quaternion threshold
  • DOC: Changelog
  • DOC: Notes on software-based GL rendering
  • MNT: Version

fsleyes-plugin-mrs 0.1.0 -> 0.1.1

  • MNT: Specify MRS layout as an entry point

FSLeyes 1.8 will support specifying custom layouts as entry points, just like how views, controls, and tools are specified. This allows FSLeyes to associate a specific layout with the library that it is defined within, and enable other plugins that are provided by that library.

Detailed history

  • MNT: Use new FSLeyes >=1.8 layout plugin feature
  • MNT: Version
  • Update docs and fix small bug.
  • Update date in changelog.
  • lint
  • Update doc version.

fslpy 3.14.1 -> 3.15.1

  • MNT: Make GIfTI metadata available

Adjust the GiftiMesh class so that all metadata stored in a GIfTI file is made available via the Meta interface.

  • ENH: Wrapper function for FSL cluster command
  • MNT: Pre-release administrative updates

Detailed history

  • MNT: GiftiMetaData.metadata is deprecated
  • MNT: convert to f-strings
  • MNT: Copy all GIFTI metadata into GiftiMesh metadata store
  • CI: Update skip-tests match
  • TEST: Don't consider "testdir" to be a test function
  • DOC: Changelog
  • RF: New Meta.meta property, nicer way to set/access metadata
  • TEST: Test Meta.meta property
  • ENH: Wrapper function for cluster
  • DOC: Changelog
  • BF: Convert to string
  • TEST: Test cluster wrapper
  • DOC: Changelog
  • MNT: Pre-release version bump
  • DOC: master->main
  • MNT: Version
  • TEST: Assume that "python" is available on the $PATH - tests run during conda build process may have a very long/invalid shebang line which causes the test to fail
  • DOC: Changelog
  • MNT: Version

fsl-base 2306.1 -> 2309.2

  • RF: Allow USR* Makefile variables to be set in the environment

  • ENH: new open_fsl_report command

  • New open_fsl_report command, for opening HTML report pages which may contain javascript, such as PNM reports.

  • Replace setup.py file with a pyproject.toml file.

  • DOC: Update changelog and version number

  • TEST: Re-organise unit tests

Re-organise unit tests - feedsRun now dynamically loads all test_*py scripts, and runs all test_* functions contained within. Also add a basic test for open_fsl_report.

Detailed history

  • RF: Allow USR* make variables to be set via environment variables
  • DOC: Changelog
  • MNT: Replace setup.py with pyproject.toml
  • ENH: New open_fsl_report command, for opening HTML report pages which use javascript
  • DOC: Changelog
  • TEST: Re-organise tests - feedsRun will load all test_py scripts, and run all test_ functions contained with. Add basic test for open_fsl_report
  • RF: Allow args to be passed to open_fsl_report.main()
  • TEST: fix test path, fix to update_fsl_release tests
  • MNT: version
  • DOC: Changelog
  • TEST: Use exes in $FSLDIR - removing option to run tests in-source for the time being
  • TEST: Fix update_fsl_release tests
  • MNT: Add --yes option to update_fsl_release to skip confirmation prompt
  • DOC: Changelog
  • TEST: Disable query_installed_packages cache. Make sure that channels are set for env update operations.

fsl-get_standard 0.2.0 -> 0.3.0

Detailed history

  • MNT: replace setup.py with pyproject.toml
  • CI: run unit tests in local project pipeline
  • DOC,ENH: Update README describing support for templates of different modality
  • ENH,RF: Update fsl_get_standard to support different image modalities. Remove hard-coded image types - manifest files can now define any image types (although "whole_head", "brain", "brain_mask" should always be present). Refactor so that argparse handles invalid values for any of image type, modality, or resolution.
  • TEST: Update unit tests
  • MNT: Version attribute moved
  • MNT: Compatibility, accounting for the exceedingly unlikely possibility that third party code is pulling verison from its original location

fsl-installer 3.5.6 -> 3.5.7

  • ENH: Allow existing ArgumentParser to be passed to parse_args

This will allow e.g. the update_fsl_release script to add additional arguments.

Detailed history

  • ENH: allow existing ArgumentParser to be passed to parse_args
  • DOC: Changelog

fsl_mrs 2.1.12 -> 2.1.13

  • Enh: fMRS group level f-tests

2.1.13 (Tuesday 5th August 2023)

  • Add group level f-tests to the fmrs_stats tool. First level f-contrasts are not yet implemented.
  • Removed / retained indices after fsl_mrs_proc unlike (and related functions) are now listed in the NIfTI-MRS headers under the key "DIM_DYN Indices".

Detailed history

  • Added higher level ftests to the flameo wrapper
  • Add ftests to fmrs_stats tool
  • Update changelog
  • Update doc.
  • Update doc.
  • Add tracking of indicies with unlike command.
  • Typo

fsl-pipe 1.0.0 -> 1.0.1

  • Fix duplicate jobs when linked placeholders are used
  • Check for warnings in tests
  • Bump version: 1.0.0 → 1.0.1

Detailed history

  • Fix duplicate jobs when linked placeholders are used
  • Check for warnings in tests
  • Bump version: 1.0.0 → 1.0.1