I'm not entirely sure what those steps are trying to do. Extract out signal from voxels in thalamus that have a positive sig? You can do that with one call to mri_segstats. This page has an example:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual_freeview

On 9/4/2020 11:56 AM, Nasiriavanaki, Zahra wrote:

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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer