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:fischl@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:astevens@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.
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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
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