Doug, I looked at the surface files by using the command -tkmedit (subject ID) brainmask.mgz -surfs -aseg. I also viewed the same surfs using the T1.mgz file. The pial surface (red line) does identify the dura as part of the cortex, but it doesn't look as bad as the aseg.mgz vois made it appear.
Cyrus -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, August 13, 2012 4:13 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Hi Cyrus, this may or may not be a problem. The cortical label in aseg.mgz is not used for this reason. Usually, the surface-based method will exclude the dura in these situations. Are the surfaces accurate or are they including dura as well? BTW, you should not be editing the aparc+aseg.mgz. doug On 08/13/2012 01:04 PM, Sarosh, Cyrus wrote: > > Hello FreeSurfer Users, > > I looked for a possible solution to my problem in the Mail Archive and found > this article referring to almost the exact same problem I am having: > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06314.ht > ml. Basically,pieces of the subarachnoid space/pia > mater/arachnoid/dura mater/skull > are being segmented as the cortex in certain slices and this occurs when it > is physically adjacent to the gray matter. Besides this point everything else > seems to be running smooth. > In the related article I found that this may be caused by the MR parameters > so I will give you the acquisition information that I know. > Theacquisitions are SPGRs, taken on either a GE 3T or 1.5T and the > resolution is 1mm isotropic. Any solutions besides going through each > series slice by > slice and making corrections would be greatly appreciated. > > Thanks, > > Cyrus > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should > not be used for urgent or sensitive issues > > > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
