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 <fis...@nmr.mgh.harvard.edu> Date: Monday, February 15, 2010 10:42 am Subject: Re: [Freesurfer] Subcortical Volume Calculation To: Hui J Yu <h...@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. > > > > > >
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