hmmm, I guess the ribbons should override the aseg w.r.t. cerebellum label as well.
On Fri, 11 Sep 2009, Kim, Miyoung wrote: > Hi, Doug. > > It is the output after autorecon3 (so yes, aparc+aseg.mgz)..... > > I found another situation similar to this (different subject) - see attached. > It seems like it might be occurring more frequently than I had suspected > earlier. > > > Miyoung > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Thursday, September 10, 2009 4:16 PM > To: Kim, Miyoung > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] editing aseg.mgz? > > 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 > > 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
