Hello, I am dealing with a problem on FreeSurfer a couple of days now. I want to fix the scull strip and I run the following commands: cd /users/Angeliki/studyname export SUBJECTS_DIR=studyname/subjid/session/T1/ recon-all -skullstrip -wsthresh 20 -clean-bm -no-wsgcaatlas -subjid FreeSurfer
Then, the command works and the part of the cerebellum that I don't need turns brown. I close it and I save the script with: gedit ~/FreeSurfer/Angeliki/run_reconalls_aut1.sh And type at the script for echo: recon-all -autorecon2 -autorecon3 -subjid FreeSurfer Finally, I submit it to the cluster with the command: ~/FreeSurfer/Angeliki/run_reconalls_aut1.sh
The problem is that even though it runs properly (and I tried to add some control points and they work), the brown part of the cerebellum does not disappear, but remains there.
Is there something I have to change?
Thank you, Best, Angeliki Tsapanou