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Washington-University / HCPpipelines

Processing pipelines for the HCP
https://www.humanconnectome.org/
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Update FSL contribution to PATH #299

Closed MichielCottaar closed 1 month ago

MichielCottaar commented 2 months ago

As of FSL 6.0.6 (release date: 22 nov 2022), the binaries are stored in $FSLDIR/share/fsl/bin, not $FSLDIR/bin

See https://fsl.fmrib.ox.ac.uk/fsl/docs/#/development/history/index?id=_606-22nd-november-2022 for more details

Including $FSLDIR/bin in the $PATH will include all the FSL-specific binaries, but also a lot of other non-FSL related ones. This can lead to confusing behaviour, where FSL versions of generic tools will be used after running source SetupHCPPipeline.sh rather than built-in versions.

coalsont commented 2 months ago

This looks like it would make the pipelines incompatible with FSL older than 2 years. Perhaps this should check whether share/fsl/bin exists and decide based on that what to add to $PATH.

MichielCottaar commented 2 months ago

That is a good point. I guess it would be slightly better to check the version number of FSL, but I'm not aware of an easy way to compare version numbers in raw bash. So, checking $FSLDIR/share/fsl/bin sounds like a good idea. I'll adjust this PR to do that.

glasserm commented 1 month ago

I am okay with accepting this. Thanks Michiel for contributing.