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
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