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FSL 6.0.7.13, 1st August 2024

file-tree 1.3.0 -> 1.4.0

Detailed history

  • ENH: enable loading of file-trees with conflicting template keys An error is instead raised when those conflicting template keys are accessed.
  • BF: fix filter_templates for duplicates
  • DOC: clarify iteration
  • Fix rich report output
  • BF: do not add templates multiple times in filter_templates
  • BF: sort keys when generating string output ensures the output is consistent
  • ENH: allow templates without any keys pointing to them. These can be used as parents for other templates
  • ENH: add override method
  • Fix code-block formatting
  • Fix overriding
  • Use multiple line to make code easier to read
  • Fix data1/data2 names to include in_ prefix
  • Update for v1.4.0 release
  • Bump version: 1.3.0 → 1.4.0

fsleyes 1.12.3 -> 1.12.4

Detailed history

  • Remove out-dated comment about installing old wxpython. [skip ci]
  • MNT: As of numpy 2.x, np.array(copy=False) now raises an error if a copy cannot be avoided
  • CI: Add a hook to run commands prior to testing - will allow me to update numpy in the CI env
  • TEST: Shouldn't be testing for exact equality
  • MNT: Apply arparse changes to python >=3.11.9 as they were backported to 3.11

fslpy 3.19.0 -> 3.21.0

Detailed history

  • ENH: New featanalysis.loadFTests and getZFStatFile functions, for getting F-test results. New loadFEATDesignFile for loading design.mat/con/fts files. String formatting fixes
  • TEST: Unit tests for loadFTests and getZFStatFile functions
  • MNT: String formatting
  • ENH: accessors for zfstats
  • ENH: Modify loadClusterResults to allow loading f-test results, accessor for f-test cluster mask file
  • ENH,BF: add accessors to FEATImage class, fix zfstats accessor
  • TEST: test loading f-test cluster results and zfstat/cluster_mask_zfstat files
  • ENH: FEATImage.ftests accessor
  • TEST: Test FEATImage f-test accessors
  • MNT: Pre-release version bump
  • BF: Missed one attribute on Cluster objects
  • DOC: Update date in changelog
  • MNT: Work-around nibabel auto-rescaling logic so that data/slope/intercept in imcp'd images is not modified
  • TEST: Test ensuring that imcp does not modify data
  • MNT: Pre-release dev version bump

fsl-base 2404.0 -> 2407.0

Detailed history

  • RF: Relax create/remove wrapper constraints to allow creation of wrappers for executables contained in child environments within $FSLDIR
  • TEST: Test creating wrappers for exes in child env
  • MNT: update comment
  • ENH: Allow additional ("extra") FSL components to be installed into an existing FSL installation with the update_fsl_release command
  • ENH: Update fslversion to support child environments
  • MNT: Don't skip extra components that already exist - attempt to update them instead
  • TEST: Test updates
  • MNT: Guard against having no revisions (occurs in test env)
  • TEST: Make sure FSL env file has conformant name. Need to list python in environment file
  • MNT: comments
  • MNT: Adjust createFSLWrapper so that it does not re-create wrapper scripts that already exist
  • TEST: adjust wrapper script unit tests, new test to make sure existing wrappers are not overwritten
  • BF: Bug in handling extra envs
  • MNT: Accept cuda argument, and a few others

fsl-feat5 2201.6 -> 2201.7

  • MNT: Adjust/simplify FILM runtime estimation The old estimation seems to massively over-estimate run time for a 'typical' modern analysis, e.g. estimating ~10.5 days for a data set of dimensions (108, 108, 72, 750) and 37 EVs.

Detailed history

  • MNT: Adjust/simplify FILM runtime estimation

fsl-installer 3.9.0 -> 3.14.0

Detailed history

  • MNT: assume that all values in manifest are strings
  • TEST: Test new str2bool helper function
  • RF: Use CUDA-specific installation progress metrics. Log progress bars, so log file contains progress tracking
  • BF: Make sure cuda_enabled flag is present for extra environmentstoo
  • BF: bugfix in devrelease file name parsing - lstrip/rstrip remove all provided characters, they do not remove sub-strings
  • RF: Move add_cuda_packages call, so that update_fsl_release has fewer things to do
  • BF: typos
  • MNT: Bump version - was incorrect in previous tag

fsl-misc_tcl 2303.0 -> 2406.0

Detailed history

  • BF: runtime passed to fsl_sub must be an integer

fsl-mist 2111.5 -> 2111.6

Detailed history

  • MNT: Bump vtk to 9.3

fsl_mrs 2.1.20 -> 2.2.0

Detailed history

  • BF: Deployment validation tagging
  • MNT: Python 3.11, numpy 2.0

fsl-pipe 1.0.2 -> 1.0.3

Detailed history

  • Remove duplicate is_singular import
  • Remove numpy import I used it to check whether a placeholder was singular, but there is already a better function for that in file-tree.
  • Fix link to FSL pipe example
  • Prevent hash error if placeholder contains list
  • Explain bug fix
  • Test running on dask
  • Actually call compute on dask graph
  • Do not check warnings raised The checks failed in python 3.12 for some reason, so just got rid of them.
  • Remove deprecated ~ for logical inversion
  • Fix which filenames should not exist
  • Bump version: 1.0.2 → 1.0.3

fsl-pyfeeds-tests 2401.1 -> 2407.0

Detailed history

  • RF: Print mmorf executable. Save fsl_sub log files to test output directory.
  • TEST: Add basic tests for truenet

fsl-pyfix 0.8.0 -> 0.8.1

  • BF: Fix default highpass (-h) behaviour Fixed the default behaviour of the -h option - when omitted, the default behaviour should be to read the highpass threshold from design.fsf (if present). But highpass-filtering was being skipped by default.

Detailed history

  • BF: Fix default highpass behaviour - default behaviour (-h omitted) should be that the highpass value is taken from design.fsf. But it was defaulting to -1 (no highpass). Also, -h -1 was not being detected, and was causing fslmaths to be passed a negative sigma, which would caus the filter to be skipped (which is intended, but if -h -1, then there's no need to call fslmaths at all).
  • MNT: warning when -h is used superfluously

fsl-sub-plugin-slurm 1.6.3 -> 1.6.4

  • Pyproject toml Update build infrastructure to use new setup tools Add linting CI job and make code more PEP8 compliant

Detailed history

  • Pyproject toml
  • When only using GRES to select GPUs it is not possible to request all GPUs of this type an better. Add warnings to reflect this - user can use --extra to define additional constraints to allow grouping of GPUs Refactor tests for new GPU functionality
  • Add documentation about the warning generated when include_more_capable is true and class_constraint false

fsl-topup 2203.4 -> 2203.5

  • Fixed bug that made sanity check on acqparams.txt reject synb0-DISCO use There is a sanity check on readout times in the --datain/--acqp files. I recently coordinated that with eddy's sanity check, to ensure they have the same view of what is sane. But that meant that registering to a distortion free image no longer worked. And that is a valid thing to do, for example in the context of synb0-DISCO. I have now fixed it so that it allows one volume to have a readout time of zero, or almost zero.

Detailed history

  • Fixed bug that made sanity check on acqparams.txt reject synb0-DISCO use

spec2nii 0.7. -> 0.8.

Detailed history

  • GE ISTHMUS/Hyper Sequence (#137)
  • MNT: Drop python 3.8 support, add 3.12, deal with numpy 2.0 (#139)
  • ENH/svs_slaser_dkd (#136)
  • ENH: twix mixed headers (#135)
  • Add support for .txt files exported by older versions of jMRUI (#133)
  • Enhance support for GE data (#132)
  • Add handling and tests for philips mega sequence. (#131)
  • BF: Correct Universal editing sequence HERMES conditions and tests for XA50 twix and RDA (#130)
  • dMRS and MEGA-sLASER fixes for PV360.1.1 (#124)
  • ENH: Validated rda orientation and CSI handling (#128)
  • Fix dicom naming bug with mixed types (#122)
  • Imporvements in philips tag handling. (#121)
  • Enh: Automatically add spectralwidth to header extension (#120)
  • Add a duecredit citation for whenever spec2nii is used (#119)
  • Update CHANGELOG.md (#118)
  • add support for GE P-file rev 29.1 & 30.0 (#117)
  • BF: RDA decoding issue (#115)
  • Add handling and tests for CSI data stored in Simens enhanced DICOM (#114)
  • Enh: Anonymisation at runtime (#113)
  • in [x, y, z] → in (x, y, z) (#105)
  • Avoid redefining Python builtins (#98)
  • Bump actions/checkout from 3 to 4 (#95)
  • Fix typos found by codespell (#93)