The easiest way would be to edit pctsurfcon in the following way
Change set wm = $tmpdir/$hemi.wm.$ext To set wm = $outdir/$hemi.wm.$ext
and
set gm = $tmpdir/$hemi.gm.$ext To set gm = $outdir/$hemi.gm.$ext
This will create ?h.wm.mgh and ?h.gm.mgh in subject/surf
doug
On 04/01/2014 12:26 PM, N. Medic wrote:
Dear FreeSurfers,
The pctsurfcon calculates the contrast between the white and gray matter using the formula below and saves the output in the ?h.w-g.pct.mgh file, which can be used for analysis.
100*(W-G) pct = --------- 0.5*(W+G)However, I would like to get separate measures of white and gray matter intensity, as well as a ratio of gray to white matter (as in the Salat 2009 and 2011 Neuroimage papers). How can this be done?
Your help will be greatly appreciated
Nenad
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