Thank you for the quick response. If you do a partial volume correction, I would think the volumes from freesurfer would be less than simply counting all voxels, but it seems to be the opposite. Any thoughts?

----- Original Message -----
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Date: Monday, February 15, 2010 10:42 am
Subject: Re: [Freesurfer] Subcortical Volume Calculation
To: Hui J Yu <hjyu@ic.sunysb.edu>
Cc: freesurfer@nmr.mgh.harvard.edu

> yes, we do a partial volume correction of the volumes,
> accounting for the fraction of the structure in each border voxel.
>
> cheers
> Bruce
> On Mon, 15 Feb 2010, Hui J Yu wrote:
>
> >Dear Freesurfer users,
> >
> >I am wondering how are the volumes calculated from stats such
> aseg.stat. When I export the aseg and do a voxel count and
> multiple the volume per voxel, my total volume is different from
> that is given by the stats. For example, the hippocampal
> volume given by aseg.stats for one of my controls is 4000 cm3,
> but when I export the aseg.mgz into matlab and do a voxel count
> (my original voxel volume is 1mm3 isotropic) for that labeled
> mask, the total volume is aorund 3000 cm3. Does freesurfer
> does some sort of intensity normalization or partial volume
> correction? Even if so, the magnitude of difference is
> large that I am puzzled.
> >
> >Thank you very much.
> >
> >
> >