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 <templateid>/mri talairach_avi --i nu.mgz --xfm transforms/talairach.xfm recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -segstats

3. fix the longs: recon-all -long <tpNid> <templateid> -talairach -segstats

Best, Martin

On Mon, 2012-08-20 at 14:47 -0400, Nick Schmansky wrote:

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 nu.mgz --xfm transforms/talairach.xfm recon-all -s subjid -segstats

this re-runs that talairach using the nu corrected image as input (which was how it was done prior to v5.1 and is how it will be done in v5.2), then regenerates the stats, where the one item that will change in the aseg.stats file will be the ICV (eTIV) calc.

Nick

On Tue, 2012-08-14 at 10:53 -0600, Cheryl McCreary wrote:

...

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

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