yes it is On Thu, 7 Oct 2010, Wang, Xin wrote:
Thank you, Allison. Is Unknown for the empty space between gyri? I did label the gray matter vertices as cortex.
Xin
From: Allison Stevens [mailto:astevens@nmr.mgh.harvard.edu] Sent: Thu 10/7/2010 12:16 PM To: Wang, Xin Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] zero cortical thickness in the lingual and precuneus
None should be the first label in the FreeSurferColorLUT.txt (it's labeled as "Unknown" with an ID# of 0). But really you should be labeling it what it truly is. Is this the gray matter you are labeling as CSF?
--
On Thu, 7 Oct 2010, Wang, Xin wrote:
one more question: I replace the mislabeled lateral ventricle with CSF because I can not find the "none" in the FreesurfercolorLUT.txt. How to change the mislabeled lateral ventricle to none?
Thank you,
Xin
From: Wang, Xin Sent: Thu 10/7/2010 12:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: zero cortical thickness in the lingual and precuneus
Hello, Dr. Fischl,
I asked this quesion about zero thickness in the sulcus next to the lateral vertricle before, and corrected the wrong label of lateral vertricle in the aseg.mgz file and added white matter between lateral vertricle and this sulcus in the wm.mgz. But the problem is still exist in some slices after multiple times of correction. We have this problem in version 4.4.X to 4.5.0. My questions are
- Do you have any additional suggestion to fix this bug?
- If not, do you have a way to exclude this problematic sulcus? In another word, can we include this sulcus in the unknown zone? I don't like to exclude entire lingual, precunneus, and pericalcarine regions from mean thickness analysis and vertex-based analysis because these three labels occupy a large part of cortex.
Thank you in advance,
Xin Wang
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu Sent: Thu 10/7/2010 11:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 80, Issue 12
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