FSL command not found after loading required modules

[ruben-stanford]

Hello,

I am attempting to use the FSL 6.0.1 module on Sherlock, graciously provided and maintained by the Poldrack lab. However, after doing ml contribs poldrack, the FSL and related packages (e.g., FEAT) do not seem to work as expected. For example:

Loading the contribs/poldrack module:

FSL and other commands do not work:

However, FSLDIR is set:

Is this a regression introduced recently? This workflow used to work for me previously. Note that ml biology fsl works, but this is for FSL 5.

[poldrack]

hi - yes, unfortunately I deleted the older version of FSL that was being linked (6.0.4), since our lab doesn't use those older versions any more. I could either reinstall 6.0.4, or point to the latest version (6.0.7 I think).

[ruben-stanford]

Hey @poldrack,

Thank you for the response. Is there any version of FSL 6 that is supported by the contribs/Poldrack module on Sherlock? I would appreciate any version of FSL 6 being available on Sherlock, since FSL 6 is the major version that I use locally and seems to be the standard for recent neuroscience papers.

Thus, I would welcome any solution that makes any sub version of FSL 6 work on Sherlock.

[poldrack]

I'll have 6.0.4 working again by end of today

[poldrack]

ok, module is working with 6.0.4 again - lmk if you experience any problems. I am also installing the latest (6.0.7.10), will let y'all know once it's available but I am leaving 6.0.4 as the default as before

[poldrack]

the latest version can now be loaded using: module load fsl/6.0.7.10

[ruben-stanford]

Thank you so much @poldrack!