Hi John,

mri_segstats is the right thing to do. It doesn't rerun the segmentation, but if you rerun the command you find can in the scripts/recon-all.log file it will do things like correct for partial volume effects, which is a big deal in the hippocampus.

cheers Bruce

On Thu, 23 Dec 2010, McLean John (NHS Greater Glasgow & Clyde) wrote:

Hi,

I have ran recon-all and got the Hippocampal volumes I desire from the aseg.stats file. However, I have manually refined some of the volumes using the tkmedit segmentation tool brushes and I now need to extract the revised volume estimates.

I believe I can run 'mri_segstats' to obtain the revised volume, this seems to run the full segmentation process again, would this be the recommended way of obtaining the revised volumes or if I'm only interested in the Hippocampal volume is there a more precise command I could run to extract only this from my revised aseg.mgz segmentation file?

Many Thanks John McLean

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