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

input sub1-base MCI

input sub2-base AD

input sub3-base HC

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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer