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