Hi Marcos, the right way of doing this is using the soft posteriors to compute the mean and variance, rather than thresholding at p=0.5. For instance, if you wanted to compute the mean and variance of the intensitites of the subiculum, you would do something like this: mean=sum(Ps.*NU)/sum(Ps); variance=sum(Ps.*(NU-mean).^2)/sum(Ps); (where Ps is the posterior of the subiculum) Cheers, /Eugenio

On Mon, 2013-06-10 at 15:12 -0300, Marcos Martins da Silva wrote:

Hi, Freesurfer Experts

After usual processing with recon-all -all we get the aseg.stats file with several data including intensity values like: normMean normStdDev normMin normMax normRange Left-Hippocampus 77.8939 7.5748 46.0000 105.0000 59.0000

How could I get similar results for each hippocampal subfield, assuming I also generated all posterior*.mgz files corresponding to each subfield? I guess I should first binarize each of the subfields file with a threshold=127 to map all the pertinent voxels, and then use these files as masks over nu.mgz and calculate the intensities values. But I do not know the best way to accomplish this after the binarize step.

Thank you in advance for any help.

Marcos _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer