Hi @Hana-Ali,
This is a flirt-specific error message, which is part of FSL, so I don’t know how to trace back their error messages to interpret them accurately. But I expect the file matching relates to their file handling via the FSLOUTPUTTYPE environment variable. What it seems to be saying is that it can’t find a file that matches the specification:
/rds/general/user/hsa22/ephemeral/camcan/atlas/glasser360mni
(which is presumably what your {atlas} expands to?) having tried:
/rds/general/user/hsa22/ephemeral/camcan/atlas/glasser360mni.nii.gz
(which presumably implies that FSLOUTPUTTYPE is set to NIFTI_GZ?). If that file does indeed exist, then I don’t know what the problem is… You may have better luck on the FSL mailing list?
By the way, I note your -ref option is missing the initial dash – I assume that’s just a typo in your post, right?
All the best,
Donald.