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 from qdec?
Thanks
Jen
On Oct 28, 2008, at 4:30 PM, Doug Greve wrote:
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 gamma.mgh
doug
Bramen, Jennifer E. wrote:
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 view this output though (<group descriptor>_thickness_fsavg.mgh). Can someone explain what this output is and how I can use it?
The other alternative is make_average_surface for each of my groups. Is that what I need to be doing? It takes a ong time to run, so I was hoping there was another way to go.
Thank you
Best regards,
Jennifer Bramen, Ph.D. Postdoc David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)206-5518 Email: jbramen@mednet.ucla.edu Campus Mail Code 176919
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Jennifer Bramen, Ph.D. Postdoc David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)206-5518 Email: jbramen@mednet.ucla.edu Campus Mail Code 176919
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