Depending upon how bad it is and what you are going to do with it, it may be a good idea to edit the brain.finalsurfs.mgz to remove the dura, then run recon-all -autorecon-pial ... doug
On 08/14/2012 11:18 AM, Sarosh, Cyrus wrote: > 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 > > -- 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
