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 group, and in each contrast directory, there will be a C.mat file with the contrast vector.
doug On Wed, 29 Oct 2008, Bramen, Jennifer E. wrote:
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: [EMAIL PROTECTED] Campus Mail Code 176919 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 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: [EMAIL PROTECTED] Campus Mail Code 176919 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
-- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
