And for fixing this in the longitudinal stream this should work:
1. you can fix the cross runs as described below (not really necessary,
as the longitudinal results do not depend on this)
2. fix the base:
cd /mri
talairach_avi --i nu.mgz --xfm transforms/talairach.xfm
recon-all -base -tp -tp .
The problem with the ICV calc in v5.1 is explained in the v5.1 Known
Issues section of the ReleaseNotes page, which i've also just updated
with notes on a workaround:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
the workaround is to type these commands:
cd subjid/mri
talairach_avi --i
Dear fs Experts,
In the most recent Freesurfer Digest (vol102, Issue13), a question regarding
ICV calculations in version 5.1.0 was raised (message 4). Can you please
expand on the problems with this? I am using version 5.1.0 and the estimate of
ICV is of interest.
Thanks,
Cheryl McCreary
o fix this?
>
> Laura
>
>
> From: natalie.h...@gmail.com [natalie.h...@gmail.com] on behalf of Natalie
> Han [zh...@stanford.edu]
> Sent: 13 August 2012 19:56
> To: Bruce Fischl
> Cc: Wisse, L.E.M.; freesurfer@nmr.mgh.harvard.edu
> Subjec
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 ch
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 tha
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.
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 sk
