I think nick has a patch he can distribute before we release 5.2 Bruce
On Aug 14, 2012, at 3:13 AM, "Wisse, L.E.M." L.E.M.Wisse@umcutrecht.nl wrote:
Hi Bruce, Thanks for the quick response. I also used FS v5.1.0. Do I need to use another version or is there another way to fix this?
Laura
From: natalie.hanz@gmail.com [natalie.hanz@gmail.com] on behalf of Natalie Han [zhan1@stanford.edu] Sent: 13 August 2012 19:56 To: Bruce Fischl Cc: Wisse, L.E.M.; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problems with ICV
Hi, Bruce, I've been using FS5.1 for segmentation analysis, after I updated the mri_segstats, the ICV does not seem to change at all, only the SupraTentorial Volume changed. If I want to use ICV and SupraTenrotial Volume for my analysis, is that OK to use FS5.1, I don't see more updated version than FS 5.1.0. Thanks. Also, is there a commandline to extract other numbers in the header of aseg.stats?
Thanks. Natalie
On Mon, Aug 13, 2012 at 9:15 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Laura,
what version of FS are you running? The ICV is estimated using the talairach xform, and there were some problems with it in 5.1.
cheers Bruce
On Mon, 13 Aug 2012, Wisse, L.E.M. wrote:
Dear freesurfers,
I tried to calculate ICV with FreeSurfer, but I encountered some problems. I first ran autorecon 1, 2 and 3, but I noticed afterwards that a few ICV values were really off. The values were really high and when I looked at brain.finalsurfs.mgz, the segmentation also included skull, eyes and sometimes even the nose and ears. (I am not sure that I should look at the brainfinal.surfs.mgz for ICV segmentation, but the segmentations seemed to correlate with the ICV values.)
So, I decided to try adjusting the watershed parameters and I also tried using gcut. I noticed that the segmentation brain.finalsurfs improved a lot, however in aseg.stats the ICV values did not change at all!
Can anyone help me with this problem?
Kind regards, Laura Wisse
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