I just wanted to add that the attached maps in the previous email, was made by the tksurfer command below. I also added the mri_glmfit command.

mri_glmfit --y cespct.nii.gz --osgm --glmdir main.wls --nii.gz --mask ../mask.nii.gz  --surface fsaverage ${space:(-2)} --cortex --fwhm 5 --no-prune

tksurfer fsaverage lh inflated -ov cache.th13.abs.sig.masked.mgh -fminmax 1.3 7

I appreciate if you could let me know your comments.

Thanks a lot!

Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Boston, MA, USA, 02129

On Jan 22, 2021, at 6:28 PM, Nasiriavanaki, Zahra <ZNASIRIAVANAKI@mgh.harvard.edu> wrote:

Hi Freesurferers

I am running mri_glmfit-sim to do multiple comparison correction with the command below. It goes through without any error. However when I view the corrected maps in tksurfer, I see some clusters in corrected map with p=2 and p=3, but I don’t see them in corrected map with p=1.3 (images attached). The contrast of interest is the same between the maps. The viewing threshold is 1.3 in p=1.3 maps and is 2 and 3 in the p=2 and p=3 maps respectively.
I’m confused. 
Could you please comment on that?

mri_glmfit-sim --glmdir main.wls --cache 1.3 abs --3spaces 
mri_glmfit-sim --glmdir main.wls --cache 2 abs —3spaces 


Thanks a lot
Mona

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Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Boston, MA, USA, 02129