I have a problem with running the 5ttgen command in my python script to premask the HCP data.
I used exactly the command from the manual:
5ttgen fsl T1w_acpc_dc_restore_brain.nii.gz 5TT.mif -premasked
But then this error appears:
5ttgen: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
5ttgen: Generated temporary directory: /tmp/5ttgen-tmp-RK5S80/
Command: mrconvert /home/ubuntu/E130-Daten/IngoHermann/111111/T1w/Diffusion/T1w_acpc_dc_restore_brain.nii.gz /tmp/5ttgen-tmp-RK5S80/input.mif
[ERROR] Environment variable FSLDIR is not set; please run appropriate FSL configuration script
I’m very new in this topic and I don’t know how to set the variable FSLDIR.
Thank you in advance!
And now a new error appears but I tried everything even this but I get this error.
[ERROR] Atlases required for FSL’s FIRST program not installed;
Please install fsl-first-data using your relevant package manager