Hi Bruce, Thanks a lot.
I have finished the running of autorecon3. I got three new files: aparc+aseg.mgz; aparc.a2005s+aseg.mgz;wmparc.mgz. What's the difference between the first two files? Which corresponds to the grey matter? By the way, I failed when using autorecon1 to do skull stripping. Besides manual correction, is there any other automatic way to correct the result(I have tried to change the threshold value, not good result)? Looking forward to your early reply. Best, Xiaoying ----- Original Message ----- From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> Date: Friday, March 5, 2010 8:41 am Subject: Re: [Freesurfer] problem on freesurfer To: Xiaoying Tang <xta...@jhu.edu> Cc: ni...@nmr.mgh.harvard.edu, Freesurfer@nmr.mgh.harvard.edu > Hi Xiaoying, > > there are gray matter estimates in aseg.mgz, but you need to run > autorecon3 to get the surfaces that let us estimate cortical gm most > accurately. > > cheers, > Bruce > On Fri, 5 Mar 2010, Xiaoying Tang wrote: > > > Hi Nick, > > > > Sorry, I am not sure whether I can successfully post my problem on > the mailing list. So I send you the email and cc it to the mailing list. > > > > I now have a problem on freesurfer. After run auto-recon2, I am > supposed to get grey matter and white matter. The white matter is in > the form of wm.mgz, but I can't find something like gm.mgz. Can you > tell me where is the grey matter? Is it aseg.mgz? > > > > Looking forward to your early reply. > > > > Sincerely, > > > > Xiaoying > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > > > > > > > > > > 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 > . 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 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.
