Your FSGD and command look correct. As for whether it is a good idea or not, I'm not sure (you're probably the best person to decide that). One  thing to keep in mind is that if there are true thickness differences you might see some differences due to partial voluming. I would also remove the mean of the thickness. You can so this with
mri_glmfit --surf fsaverage lh --osgm --y lh.thickness.sm10.mgz --o glm.osgm.lh --eres-save :
Then use glm.osgm.lh/eres.mgh as the PVR

On 1/8/2020 9:45 PM, Vicky Shi wrote:

        External Email - Use Caution        

Dear Freesurfer team,

I am running the glm analysis on CBF maps. I have two class and I want to see the group difference regressing out the cortex thickness. I know that I can add the average cortical thickness as one covariable in FSDG file. However, I think it might worth trying to do this with GLM by using a per vertex regressor (thickness). 

My fsgd file is like below:

Class Patient
Class CTL
INPUT subj1 Patient
INPUT subj2 CTL
....

My command is below: 
mri_glmfit --y lh.fsaverage.cbf.sm10.mgz --fsgd fsgd.txt --C contrast.mtx --glmdir lh.output.glmdir --surf fsaverage lh --pvr lh.thickness.sm10.mgz

My contrast matrix is -1 1 0. 

I am wondering if what I do is correct or not. Does it make sense or I should use the mean thickness as regressor? 

Thank you for your time!

Best regards,
Vicky




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