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: gr...@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 > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > 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. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
