Summary of what happened:
When I try to call any fsl commands after properly defining and sourcing FSLDIR, my system seems to try to call an older, non-existing version of fsl. See below outputs of just calling a random command ‘bet’, and when including the full path to bet (/Users/admin/fsl_v6.0.6/bin/bet).
Command used (and if a helper script was used, a link to the helper script or the command generated):
(base) bash-3.2$ topup
/Users/admin/fsl_v6.0.6/share/fsl/bin/topup: line 2: /Users/admin/fsl/bin/topup: No such file or directory
(base) bash-3.2$ /Users/admin/fsl_v6.0.6/bin/bet hifi_nodif hifi_nodif_brain -m -f 0.4
/Users/admin/fsl_v6.0.6/bin/bet: /Users/admin/fsl_v6.0.6/bin/remove_ext: /Users/admin/fsl/bin/python3.11: bad interpreter: No such file or directory
/Users/admin/fsl_v6.0.6/bin/bet failed during command:hifi_nodif hifi_nodif_brain -m -f 0.4
Version:
6.0.6
Environment (Docker, Singularity / Apptainer, custom installation):
local, MacOS Sonoma 14.6.1 (intel)
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Relevant log outputs (up to 20 lines):
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