Hi Doug,

I spoke too soon. I tried to follow your advice and run either command:

In a terminal, cd to the GLM directory inside qdec directory and then cd to the folder of the contrast of interest and run
mri_segstats --id 1 --slabel fsaverage lh yourlabel --i gamma.mgh --sum yourlabel.sum
the output yourlabel.sum will have information about the label including the mean gamma (gamma is a map of the contrast values).

Along those same lines, you can run

mri_segstats --id 1 --slabel fsaverage lh yourlabel --i y.mgh --avgwf yourlabel.dat
y.mgh should be there already and is a stack of thickness maps for all your subjects
the output yourlabel.dat will be a single column with the average thicknesses for each subject

..... however the error message I receive is that y.mgh could not be opened...and I also don't seem to have a gamma.mgh file?

Here is the error message, I received:

mri_segstats --id 1 --slabel fsaverage lh lh.Temporal_lobe.label --i y.mgh --avgwf lh.Temporal_lobe.label.dat
sysname Darwin
hostname fmris-Mac-Pro-2.local
machine x86_64
user     fmri
Constructing seg from label
Loading y.mgh
mghRead(/8000_series/8000_series/qdec/example_contrast/y.mgh , -1): could not open file.
Filename extension must be .mgh, .mgh.gz or .mgz
ERROR: loading y.mgh
fmris-Mac-Pro-2:example_contrast fmri$ ls
X.mat                lh-Avg-Intercept-thickness    qdec.fsgd
Xg.dat                lh-Avg-thickness-Age-Cor    rstd.mgh
beta.mgh            lh-Diff-1-0-Cor-thickness-Age    rvar.mgh
contrasts            lh-Diff-1-0-Intercept-thickness    sar1.mgh
contrasts.sig.mgh        lh.Temporal_lobe.label        surface
dof.dat                lh.Temporal_lobe.label.dat    y.fsgd
error.log            mask.mgh            y.mgh
fwhm.dat            mri_glmfit.log

thanks so much for your help:

cat