Guang,

You are correct in noticing that the segstats stage appears to run during -autorecon3. It was moved to run during that stage, but the flags to enable it exist in -autorecon2, so that needs to be updated for the next freesurfer release.

Nick

On Mon, 2009-10-05 at 17:47 -0500, Guang Zeng wrote:

Hi, there,

I am looking at the volume size of front pole . In lh.aparc.stats, this volume is 590, while in wmparc.stats (it is called ctx-lh-frontalpole), this value is 610, which one is accurate?

Thanks a lot!

BTW:

In FreeSurfer Tutorial : Process Flow (http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable)

The follwing command is called at the end of recon-all -autorecon2

mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 006_S_0547_20070924 --surf-wm-vol --ctab /home/m047599/freesurfer-install/freesurfer/ASegStatsLUT.txt

However, when I looked at the recon-all.log file, it is called at the very end of autorecon3, am I right?

Guang

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