External Email - Use Caution 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. < dgr...@mgh.harvard.edu> 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: > > 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 > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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