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
