make_average_subject creates a new subject from its inputs (three in your case). the recon-all -qcache option samples the values from a subject onto the fsaverage subject. so since the fsaverage subject and your uh3 average subject are different surfaces, the vertex numbers wont match. though if you were to sample your uh3 measurements onto fsaverage, then those numbers should match, although not perfectly (the -qcache method is more accurate).

n.

On Mon, 2010-08-30 at 18:01 -1000, Jeff Sadino wrote:

Hello,

I issued this command to make an average subject: make_average_subject --subjects 2101 2102 2103 --out uh3

I wanted to verify the average thickness file is what it sounds like. I used the recon-all -qcache on each subject individually, read the fwhm0 thickness files into matlab, and averaged vertex #100. However, when I look at vertex #100 from the uh3 surf folder, the numbers don't match. What is the reason for this? I am using freesurfer 4.3.1.

Thank you, Jeff Sadino _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer