[Freesurfer] mri_segstats quetsion

Dear Freesurferers

Hi

I am trying to extract the BOLD signal values from a functional subcortical area. I did the below steps to make the functional thalamus ROI and then used the mri_segstats to extract the BOLD signal from it. I would like to know 1-if my approach is correct? 2- should I use “lhthal3” as a mask? if so, what should I use as an input? 3-I see that the “mri_segstats” outputs one value for each voxel inside my ROI, is there a way to get one value across the whole ROI (lhthal3.nii.gz)?

fslmaths 'aseg.nii.gz' -thr 10 -uthr 10 'lhthal.nii.gz' fslmaths 'lhthal.nii.gz' -mul 'sig.nii.gz' 'lhthal2.nii.gz' fslmaths 'lhthal2.nii.gz' -bin 'lhthal3.nii.gz'

mri_segstats --seg aseg.nii.gz --i lhthal3.nii.gz --sfavg this.txt

Thanks a lot M0na

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