When a 4D image is provided to an input intended for 3D images, behaviour has reverted to "FSL5" usage in that the input will be truncated to a 3D volume, with an alert to highlight this has taken place.
New tools
swe: a tool for the analysis of longitudinal and repeated measures neuroimaging data based on the sandwich estimator.
XTRACT: a command-line tool for automated tractography in humans and macaques.
avwutils
Fixed ANALYZE support in fslchfiletype, plus fully report all known formats ( including NIFTI2 ).
Better fslstats output formatting with atlas masks.
Allow use of non-continuous atlas mask labels in fslstats.
basil
Performance improvements.
bet
Exit gracefully (with relevant error messages) if expected ouput file is not written
Fixed -B option where skull images were being generated even though not requested
bianca
Fixed nibabel deprecation issue.
config
Unified all machine configurations (auto detects most machine differences now).
Updates for multi-format eddy build.
distbase
FSL build improvements
fabber
Fix compiler warnings.
Update documentation.
Update builds for FSL 6.0.x.
General performance improvements.
fdt
Update fdt GUI to match multi-shell/single-shell defaults.
feat
Fix model setup wizard for randomise groups.
flirt
Removed interactive coordinate input for img2imgcoord, and img2stdcoord.
fsl_deface
Performance improvements.
Removed deprecated option in fslreorient2std call.
lesion_filling
Updated help text.
Added check for matching input image sizes.
Added check to make sure lesion masks are within white matter mask.
Added -c (--components) option to save each lesion as a separate image.
melodic
New version of dual_regression.
miscvis
New option for choosing optimal slice in slices_summary.
mist
Only run brainstem training if given correct modalities.
MSM
Fixed build for FSL 6.0.x.
oxford_asl
General performance improvements.
Added unit tests.
post_install
FSLeyes is now installed via the main fslpython environment.
Eddy configuration script for Linux ($FSLDIR/etc/fslconf/configure_eddy.sh). Automatically sets symlinks to eddy_openmp > eddy and eddy_cudaX.X > eddy_cuda.
Added fmrib-unpack to fslpython.
Added pyfeeds to fslpython.
sgeutils
General improvements.
utils
Updated boolean option handling for all FSL commandline programs.