Hi all,

I’m trying to compute cortical thickness using mris_thickness (stable 5), but 
getting slightly different results from the recon-all 5.1.0-amd64-2.13 
(mri_make_surfaces, stable 5).

Hinted from an old thread: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05994.html, I 
set the switch “-N 20", but it returns  different values: 50% of vertices have 
identical values with the cross-correlation of about 0.98 and RMS of 0.08 mm, 
which is of course very high, but a bit odd while I was expecting nearly 
identical results. When I checked the scatter plots, the mris_thickness returns 
a bit smaller values for many vertices than the standard result. Is this 
somewhat expected difference between mri_make_surfaces and mris_thickness?

Also I found that mri_thickness reads “?h.gray”, not “?h.pial”. As I assumed 
that it reads “?h.pial” and “?h.white” to compute thickness, so I just linked 
“?h.pial” to “?h.gray”.  Is this assumed input for mris_thickness?


Best regards,
-- 
Seung-Goo KIM

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