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
<znasiriavan...@mgh.harvard.edu<mailto:znasiriavan...@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
<PastedGraphic-1.tiff>
Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Boston, MA, USA, 02129
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