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6.0.7

6.0.7, 14th July 2023

fsleyes 1.6.1 --> 1.7.0

  • New colour range option (available via the --colourRange command-line option) which can be used on vector overlays when colouring them by a secondary image, to specify the mapping between the voxel intensities and the colour map.
  • New Show slice location option, allowing the location of each slice to be displayed in the lightbox view.
  • Changed the --initialDisplayRange command-line option to have the same behaviour as the --displayRange option - by default, the values will now be interpreted as raw intensities. Values can be specified as percentiles by appending a % to the high value.
  • Colour map and lookup table files may now have a .txt suffix instead of .cmap / .lut.
  • Colour map interpolation will now be applied to the colour bar shown in the ortho/lightbox/3D views.
  • Changed the behaviour of the Clip by and Modulate by settings for volume overlays - when clipping/modulating by a secondary image, and a negative colour map is in use, the absolute values of the secondary image are now used for clipping/modulation.
  • Changes to the mechanism used to save screenshots/movies, which should make the process more robust.
  • Fixed some issues with parsing command line arguments for RGB vector and complex images.
  • Fixed an issue with plotting the MELODIC power spectrum for data with an odd number of timepoints.
  • Fixed an issue when passing a colour map file path to the --negativeCmap option.
  • Fixed an issue related to loading NIfTI qform matrices which arose with nibabel >= 5.1.0.
  • Fixed an edit mode issue where a drawn line would have gaps in it.
  • Some minor fixes which allow the overlay type of a NIfTI image to be changed whilst it is being edited.
  • Fixed a small issue with volume overlays sometimes not being refreshed.

fslpy 3.11.3 --> 3.13.2

  • New scaleAtOrigin option to the affine.compose() function, which allows the origin to be preserved by scaling parameters.
  • New runfunc() function which can be used to execute a Python function in a separate process (or as a submitted cluster job), via the func_to_cmd() function.
  • New keys(), values(), and items() methods on the Cache class.
  • The run.func_to_cmd(), run.hold(), and run.job_output() functions have been moved from fsl.utils.fslsub to the fsl.utils.run module.
  • The fsl.utils.fslsub module has been deprecated, and scheduled for removal in fslpy 4.0.0.
  • The fsl.scripts.Text2Vest now handles column vector inputs correctly.
  • The tempdir() function was not changing back to the original working directory when the override argument was used.
  • New randomise() wrapper function.
  • The fslmaths() wrapper function now allows the -dt and -odt options to be set.
  • Assertions (from the assertions module) called within wrapper functions are now disabled if the command is to be submitted via fsl_sub.
  • The Image class will now resolve symlinks when loading images from file.
  • The fslstats() wrapper no longer overwrites the log option that is passed to run(), if a wrapperconfig() context is active.

fsl-add_module 0.4.0 --> 0.5.0

  • New command to generate/update a manifest from a set of files
  • Rename Plugin.termsOfUse to Plugin.terms_of_use, so naming is same in code and JSON
  • Ability to refer to FSL course / grad course manifests by alias
  • Add support for a "size" field

fsl-base 2303.2 --> 2306.1

  • New --conda options for update_fsl_package/release to prefer conda over mamba
  • New fslnotebook alias
  • New custominstall make rule - can optionally be defined in project Makefile for any custom installation steps (e.g. flirt/feat5 "schedule" rules).
  • Adjust the update_fsl_package so that it does not call conda with --freeze-installed or --no-channel-priority - they cause too much problems; in particular, conda seems to dislike being asked to install/update anything if it is not allowed to update ssl/certificates (which it can't do when called with --freeze-installed).

fsl-bet2 2111.2 --> 2111.4

  • ENH: bet4animal from Takuya Hayashi
  • add h2c function and --ct option

fsl-bianca 2209.2 --> 2209.3

  • BF: Removed breaking .nii.gz from remove_ext call

fsl-feat5 2201.4 --> 2201.5

  • MNT: Replace "defaultfiles" with "custominstall", so it gets executed at install time, not build time.

fsl-flirt 2111.1 --> 2111.2

  • MNT: Some additional dc calls that were missed in the code audit
  • MNT: Use new "custominstall" rule, which gets executed by make install - the schedule rule was being executed at build time.

fsl-get_standard 0.1.0 --> 0.2.0

  • Don't absorb system exit
  • raise exception if an unknown resolution is requested

fsl-giftiio 2111.0 --> 2111.1

  • MNT: Pre-declare one nifti_ function which was being implicitly used in gifti_tool.c
  • MNT: Add an alternative header for C++

fsl-installer 3.4.1 --> 3.5.3

  • New --conda option to use conda instead of mamba
  • Print an error message on attempt to install FSL < 6.0.6
  • New hidden --debug option which enables super verbose logging on conda/mamba
  • Use pwd module instead of op.expanduser to determine user home directory
  • New hidden --root_env option to disable automatic --no_env when run as root. Adding primarily for testing purposes
  • Adjust defaults when installer is called as root - install to /usr/local/fsl/, and don't modify shell profile

fsl-mist 2111.3 --> 2111.5

  • MNT: Update for nibabel 5 API
  • MNT: VTK to 9.2

fsl_mrs 2.1.0 --> 2.1.6

  • Merge branch 'enh/fmrs_model_improvements' into 'master'
  • Update changelog info
  • Test tweaks
  • Fix one fo the new tests.
  • lint
  • Add more informative errors in dynamic fitting module and tests.
  • Add very basic tests for scalings.
  • First pass at scaling of dynamic results.
  • Remove debug logging
  • Add ability to form betas with different parameter categories
  • Better and tested linewidth estimates.
  • Add model performance parameters to dynamic output.
  • Merge branch 'enh/mrsi_coil_comb' into 'master'
  • Fix phase test.
  • Update changelog date.
  • Final set of coil combine tests. cov/noise extended to commandline scripts.
  • Update docs.
  • Add noise and covariance options to coil combine in fsl_mrs_proc
  • lint
  • Further testing
  • Update denmatsim commit.
  • New structure for mrsi and tests for coil combination
  • Merge branch 'bf/fsl_proc_apodise' into 'master'
  • Typo
  • Fix non working fsl_mrs_proc apodize
  • Merge branch 'bf/fsl_summarise_names3' into 'master'
  • [skip-tests] attempt 3 at summarise naming fix.
  • Merge branch 'bf/fsl_summarise_names2' into 'master'
  • [skip-tests] attempt 2 at summarise naming fix.
  • Merge branch 'bf/summarise_naming' into 'master'
  • Improved name ID for directories with subdirectories.
  • Merge branch 'bf/qc_warnings' into 'master'
  • Update QC detrending.
  • Merge branch 'enh/basis_in_report' into 'master'
  • Update report with new basis view.
  • Merge branch 'bf/fsl_summarise_conj' into 'master'
  • Update install instructions.
  • Ensure conjugation of basis in summarise matches that in fitting.
  • Merge branch 'bf/matplotlib_grid' into 'master'
  • Update changelog version date.
  • Fix depreciation bug in plotting.
  • Merge branch 'enh/x_nuclei' into 'master'
  • Update tests for new extension in symlinks.
  • Minor fixes for x-nuceli and symlinks
  • Updates for x-nuclei handling

fsl-newimage 2203.8 --> 2203.9

  • BF: samesize shouldn't write to cerr

fsl_sub 2.7.5 --> 2.8.3

  • Merge branch 'shell_to_files_default' into 'master'
  • Return default of shell log output being
  • Add license file Change development status
  • Bump version number
  • Fix bad indentation
  • Testing an file opened for writing is not safe on Linux hosts Test for non-file redirecting exception not matching generic error message
  • Fix utils tests
  • Make sure exception tests are outside of with block
  • Merge branch 'mnt/pypi-publish' into 'master'
  • Fix _run_job test
  • Remove Python 3.6 from requirements
  • MNT: add long_description to setup call
  • TEST: Work around strange mock conflict in python 3.11
  • CI: Remove py36, add py310+311 to tests. Add build+deploy pypi package jobs
  • MNT: Change license to Apache, update supported pyvers
  • Make shell runner output to controlling console
  • Linting
  • Improve handling of thread requests on SLURM
  • Update template to suggest shutil.move as this supports moving files across file systems
  • Add some debug messages to configuration loader Lint clean up
  • Add check for empty queues

fsl_sub_plugin_sge 1.5.2 --> 1.5.4

  • Switch to Apache 2 license Make Python 3.7 earliest supported version
  • Merge branch 'mnt/pypi-publish' into 'master'
  • Update setup.py to require python 3.7
  • MNT: revert name changes
  • MNT: fsl_sub -> fslsub
  • CI: Need fsl_sub
  • CI: Pipeline config for unit tests and pypi build+publish
  • MNT: Change name, change license to Apache, update python versions
  • Merge branch 'mnt/qsub-output' into 'master'
  • MNT: Ignore additional messages emitted from qsub when scraping job ID
  • Use warnings not logger.warn
  • Ensure fsl_sub 2.7 is installed
  • Merge branch 'master' of git.fmrib.ox.ac.uk:fsl/fsl_sub_plugin_sge
  • Add method to report whether the plugin suggests GPU config
  • Merge branch 'master' of git.fmrib.ox.ac.uk:fsl/fsl_sub_plugin_sge
  • Add configuration option to specify that the plugin supports parallel environments.

fsl_sub_plugin_slurm 1.4.4 --> 1.6.1

  • Fix issue #7 'jobhold' of empty list/tuples is interpreted as a valid job hold list This causes the slurm submission to be invalid. Add additional input validation and associated tests.
  • Fix minor linting issues
  • Improve reliability of tests against time based output
  • Switch default for job dependencies to 'afterany' from 'afterok'. This is the SLURM default Introduce option/environment variable to control above Add ability to specify complex SLURM job holds via the -j option. Refactor code which builds the dependency argument to simplify testing Add tests for job holds
  • Bump version number
  • Add ability to retain the job script on failure to submit Resolves issue #6
  • Move minimum python supported version to 3.7 Add license file
  • Merge branch 'mnt/pypi-publish' into 'master'
  • Update setup.py to require python 3.7 as per header
  • MNT: revert name change
  • CI: Pipeline config for unit tests and pypi build+publish
  • MNT: Change name, change license to Apache, update python versions
  • Merge:
  • Fix specification of constraints Add mem/cpu-per-gpu support
  • Merge branch 'bf/get_queue_gres' into 'master'
  • BF: Splitting wrong string

fsl-surface 2111.0 --> 2111.1

  • Fixed some typo's in stdout text from surf2surf

fsl-topup 2203.1 --> 2203.2

  • New config file that works a little better on data with large and sharp distortions

fsl-xtract 1.6.2 --> 1.6.4.1

  • Added xtract_qc, add subcortical to blueprint