Thanks for that suggestion. The command now works; however, I don't see any change when I run the BET at different parameters. I am correct to look at the T1_biascorr_brain.nii.gz right? This is the output file that we should use?
I also see no differences when I look at the different T1_biascorr_brain_mask.nii.gz files.
When I used my old scripts I can see a difference between the _brain and _brain_mask files at different BET levels.
Any suggestions as to what might be going wrong?
All help gratefully appreciated :)