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 >
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