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
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
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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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Tsapanou, Angeliki