For GM volume and thickness, you will certainly want to fix it. Given how big the PET voxels are, it might not be such a big deal for that. To fix it, you would edit the dura from the brain.finalsurfs.mgz and run recon-all with -autorecon-pial. This will fix aparc+aseg and re-generate the stats files. doug
On 08/14/2012 01:40 PM, Sarosh, Cyrus wrote: > Doug, > > Well we want to use the stats information for gray matter volume and > thickness of certain vois and we want to use the aparc+aseg file to run PET > image analysis to collect data from certain vois. Would performing the given > actions correct any incorrect data in the stats files and create a new > aparc+aseg.mgz file or will this require separate actions? > > Thanks, > > Cyrus > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Tuesday, August 14, 2012 11:28 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz > > > 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.h >>> t 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 > ********************************************************** > 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
