Doug, I edited the dura from the brain.finalsurfs.mgz file using the command tkmedit (subject ID) brain.finalsurfs.mgz -aux T1.mgz -surfs and going through the necessary slices that need fixing and erase the dura. I then ran this subject with the command recon-all -subjid (subject ID) -autorecon-pial. Looking at the date modified information it appears that new stat files were created, but no new aparc+aseg.mgz file was created. I loaded the brain.finalsurfs.mgz file, which contained a modify date of when I ran the new recon-all command and it looked identical to the original brain.finalsurfs.mgz file, so all of my edits were gone and all of the surfs were incorrect just like before. Also, loading the aparc+aseg.mgz file it looks identical to the previous aparc+aseg.mgz, so no changes were made. Looking at the log it appears my edits were useless because the first step that runs is the -maskbfs step which appears to generate the brain.finalsurfs.mgz file. So, do I need to edit a different file or was my command line incorrect?
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 1:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz 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 ********************************************************** 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
