There should be multiple contrasts, one of the contrasts should be for
group1, one for group2, and one for the difference (may be
more). Sorry, I can't remember what names they are called off the top
of my head. There will be an Xg.dat file with the design matrix to
show which regressor is which
When I look in the contrast folder, there is only one gamma.mgh image, but I
have two groups. I am assuming this is the mean thickness, or the mean
difference in thickness between groups. How do I get it to save out one file
for each group? Where is there a good explanation of the output files
If you go into the qdec output directory, you will find a contrast for
each group (class). In the contrast directory, you will find a file
called gamma.mgh. This will be the average thickness for the group. You
can load it into tksurfer, something like:
tksurfer fsaverage lh inflated -overlay
Dear Freesurfer List
I want to look at the average thickness maps for each of my groups, not just
the statistical maps displayed by qdec. I think I found a tool that can do
this. I used mri_preproc and a list of subjects instead of a single subject,
and now have the output. I do not know to vi
