Thank you. One more question, is there any way to check if this affect the surfaces after running recon-all -all?Or I need to complete the whole analysis before looking into this?Cheers,Pablo
Date: Tue, 3 Sep 2013 11:07:36 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: No brain tissue after recon-all all
Yes, that is just some eyeball that has not been stripped. It is ok as long as it does not affect the surfaces. doug
On 09/03/2013 10:54 AM, pablo najt wrote:
Hi Doug, Thank you very much for your output about my output files. Yes, I understand that these images are skull stripped. But since there are possibilities of error in the skull stripping process I was concern about extra no brain tissue being included in the output.
I think the location of the tissue I was referring was mistaken. To make it clearer I have circled (in red) the specific area in the images attached I have concerns about not being brain tissue.
I noticed that this repeats in several other of my subjects and I wanted to make sure it is fine.
Best, Pablo
Date: Tue, 3 Sep 2013 09:50:06 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] No brain tissue after recon-all all
Hi Pablo, this is a skull stripped image. In the human brain there
is no
brain tissue ventral to the orbital frontal areaso any tissue there has been stripped away. doug
On 09/02/2013 12:49 AM, pablo najt wrote:
Dear FS experts, I have a doubt about a potential registration problem after running recon-all -all. I noticed that one of the image outcome when opened with tkmedit shows no-brain tissue (perhaps eye tracts) ventral to orbitofrontal areas. I have attached snapshots to illustrate the
image.
I would greatly appreciate your output on this since I have no experience with FS and I am not sure what to expect. I would like to enquire whether I should be concerned about this image or if this is not a problem.
Many thanks, Pablo
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