Does it look that way on the aparc+aseg.mgz? Kim, Miyoung wrote: > Hi. > > I wasn't sure if my previous email (below) went through - essentially we have > a cortical occipital area that Freesurfer, upon segmentation, labels it as > cerebellum even though the pial surface appears to have been outlined > correctly (happened twice on the same data!) - I was under the impression > from the responses that the parcellation is performed using the surfaces so I > went ahead to recon3 - unfortunately that part of the cortex is still labeled > as cerebellum (see attached). > > One of my colleagues told me that she saw instances where the pial surface > would cut into the cerebellum - can editing the aseg.mgz fix both issues? If > so would you please direct me to the place on the Wiki page that details this > process (sorry - I wasn't able to find it)? Thanks much in advance!! > > > Miyoung > > -----Original Message----- > From: Kim, Miyoung > Sent: Tuesday, September 08, 2009 2:16 PM > To: 'Bruce Fischl' > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] (no subject) > > Hi, Bruce. > > Thanks for your reply - it appears that this has happened before (though I'm > not exactly certain how often) and we suspect it could happen again in the > future. You mentioned editing the aseg.mgz - would you point us to the place > on the Wiki page that details how this is done and also, can the editing be > accomplished without compromising the global GM/cerebellar/etc. volumes > significantly? Please let us know what you think. Thanks in advance!! > > > Miyoung > > -----Original Message----- > From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] > Sent: Friday, September 04, 2009 7:28 PM > To: Kim, Miyoung > Cc: Allison Stevens; freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] (no subject) > > Hi Miyoung, > > you can always edit the aseg.mgz if you want. Do you find this happens > frequently? That hasn't been our experience. > Bruce > On Fri, 4 Sep 2009, Kim, > Miyoung wrote: > > >> Thank you Allison and Bruce for your feedback! >> >> Some follow-up questions if I may - are the volumes for the gray matter and >> the cerebellum as indicated in the aseg stats file reliable and thus usable >> (e.g. can we use the GM volume in the file if it's labeled as cerebellum/use >> the cerebellum volume if it's labeled as GM)? If not how should we rectify >> this, and at which point must that be done (I've already gone ahead and >> begun recon3 without editing - can this be fixed post-recon3?)? Please let >> me know what you think. >> >> Thank you once again in advance - Happy Labor Day weekend! >> >> >> Miyoung >> >> -----Original Message----- >> From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu] >> Sent: Friday, September 04, 2009 12:06 PM >> To: Kim, Miyoung >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] (no subject) >> >> The parcellation is created using the surfaces and a cortical atlas so you >> shouldn't have to worry about the subcortical segmentation overlabeling >> like that. Take a look at the aparc+aseg.mgz in tkmedit. >> >> -- >> >> On Fri, 4 Sep 2009, Kim, Miyoung wrote: >> >> >>> Hi. >>> >>> Just a quick question - is cortical parcellation performed based on the >>> pial line (red line) or the cortical segmentation (brown shade)? The >>> reason for this question is that after recon2 we have an area in the lower >>> occipital cortical region that is shaded as "cerebellum" (see attached) >>> although the pial line seems to have correctly outlined it. Is this a >>> potential problem that we need to fix and if so what should we do? Thanks >>> for your help in advance! >>> >>> >>> Miyoung >>> >>> >>> ________________________________ >>> This message contains confidential information and is intended only for the >>> individual named. If you are not the named addressee you should not >>> disseminate, distribute or copy this e-mail. Please notify the sender >>> immediately by e-mail if you have received this e-mail by mistake and >>> delete this e-mail from your system. E-mail transmission cannot be >>> guaranteed to be secure or error-free as information could be intercepted, >>> corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. >>> The sender therefore does not accept liability for any errors or omissions >>> in the contents of this message, which arise as a result of e-mail >>> transmission. >>> >>> >> This message contains confidential information and is intended only for the >> individual named. If you are not the named addressee you should not >> disseminate, distribute or copy this e-mail. Please notify the sender >> immediately by e-mail if you have received this e-mail by mistake and delete >> this e-mail from your system. E-mail transmission cannot be guaranteed to be >> secure or error-free as information could be intercepted, corrupted, lost, >> destroyed, arrive late or incomplete, or contain viruses. The sender >> therefore does not accept liability for any errors or omissions in the >> contents of this message, which arise as a result of e-mail transmission. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > This message contains confidential information and is intended only for the > individual named. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > immediately by e-mail if you have received this e-mail by mistake and delete > this e-mail from your system. E-mail transmission cannot be guaranteed to be > secure or error-free as information could be intercepted, corrupted, lost, > destroyed, arrive late or incomplete, or contain viruses. The sender > therefore does not accept liability for any errors or omissions in the > contents of this message, which arise as a result of e-mail transmission. > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
