Hi Bruce, Thank you for your respond. It was good that it was 'brown' but after re-running it, it was staying brown. Thankfully, after days of unsuccessful trials, I started everything from the beginning and finally it worked! Thanks, Angeliki
-----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, November 18, 2015 2:42 PM To: Freesurfer support list Subject: Re: [Freesurfer] FreeSurfer question Hi Angeliki not sure if anyone answered, and also I'm not sure that I understand. If the cerebellum is "brown" in the aseg.mgz that is good - it should be. Is there a problem with the skull stripping that you are trying to fix? cheers Bruce On Thu, 12 Nov 2015, Tsapanou, Angeliki wrote: > > 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 > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
