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,
Qdec doesnt support three groups, so you'll need to use the commandline. Typing 'mri_glmfit --help' will display some output text. y.mgh is an input file. See also for examples:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
Nick
On Tue, 2014-06-10 at 13:37 +0100, 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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Elijah Mak -
Nick Schmansky, MGH