It can be dods or doss. If you don't specify, then it will use doss. To
specify, add doss after the fsgd file
On 1/29/2020 10:53 AM, Vicky Shi wrote:
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Hi Doug,
Thank you so much for your respond. Greatly appreciate it!!
I have one more question. If I run glm with FSGD and contrast file
mentioned in my previous email, it should be DOSS, correct? However,
when I tried to run it using the same FSGD, contrast and command
mentioned in my previous email, the screen prints are telling me it is
DODS as below:
INFO: gd2mtx_method is dods
I just want to confirm that I am using DOSS in this condition. And, if
I want to use DODS, I will have to make two thickness file as -pvr
inputs for each group, is this correct?
Thank you so much for your time.
Vicky
On Fri, Jan 10, 2020 at 11:22 AM Greve, Douglas N.,Ph.D.
<[email protected] <mailto:[email protected]>> wrote:
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:
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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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