Great. thanks Doug! Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129
On Sep 4, 2020, at 1:07 PM, Douglas N. Greve <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote: 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<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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