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Fixes to containers FSL dependency #2929
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- Minified FSL download updated to FSL version 6.0.7.7. - Add ${FSLDIR}/share/fsl/bin to PATH rather than ${FSLDIR}/bin. - Container minification process now appropriately captures eddy_quad command, as well as the softlink selected by its shebang.
@anaharrismatnez @jhuguetn: If you want to try |
That's great, thanks @Lestropie! We will and will give you some feedback. |
The minification container is now pulling a newer version of ANTs because the existing version was failing to compile (don't recall the specifics, but every time I tried to change one thing to get minification to work something else broke). However that change was only made for the sake of allowing me to re-run the minification process for FSL. That updated ANTs version has not been uploaded to OSF, and the MRtrix3 container continues to download the same minified version of ANTs as the |
Thanks @Lestropie, we were able to run |
Most likely, that warning is due to the issue mentioned in this post. |
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Should prevent appearance of error: /bin/bash: /opt/fsl/lib/libtinfo.so.6: no version information available (required by /bin/bash)
Closes #2921.
See also MRtrix3/containers#26, which includes changes necessary to produce the minified FSL dependency that this change then downloads from OSF.
While the container minification process intended to capture EddyQC's
eddy_quad
, the fact that it was not being properly executed was missed becausedwifslpreproc
does not return non-zero if it fails to execute.Unfortunately I couldn't easily resolve just this one thing. I've ended up having to update the FSL version as well. Which is not fantastic for a patch MRtrix update, since there's some chance of a change in behaviour out of our control.
Regarding #2921, if this change is deemed acceptable I can push it to DockerHub as
latest
, which would make it easy for people to access immediately but without necessitating an MRtrix patch update.