glad to hear it
Bruce
On Wed, 18 Nov 2015, Tsapanou, Angeliki wrote:
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
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