The y.mgh file is the "stack" of inputs (ie, each frame is a different map). In your case, assuming you want to do a thickness study, you would run mris_preproc and use the --fsgd option and specify --meas thickness (and set the other needed options), and mris_preproc will produce a stack for you. You can smooth the stack and hand the result off to mri_glmfit
doug
On 6/10/14 2:37 PM, Elijah Mak wrote:
Hello FS experts,
I have 3 groups, e.g : normal, MCI, and AD. Am I correct in my understanding that QDEC would not be applicable here?
In my subjectdir, I created a folder for mri_glmfit analyes called FSGD. In that folder, I have the FSDG file and the relevant contrasts.
GroupDescriptorFile 1
Class HC Class MCI Class AD
inputsub1-baseMCI inputsub2-baseAD inputsub3-baseHC
My contrast is a simple [1 0 -1] for HC > AD. I called it HC-AD.mtx and saved it in the FSGD folder.
Then, in the SUBJECTdir/FSGD folder, I run the mri_glmfit command as follows:
mri_glmfit --glmdir fsgd/ --y y.mgh --fsgd g3v0.fsgd --C normal-ad.mtx
My question is, what is y.mgh as shown in the examples on the Wiki? It is supposed to be an input file, but what file is this?
Thank you very much! Best Regards, Elijah
--
Elijah Mak, Gates Scholar
PhD Candidate *|* Psychiatry
University of Cambridge *| *Department of Psychiatry
Trinity College, Cambridge, CB2 1TQ
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