Load $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz into freeview and find
the voxel where you want it to be centered. Then run
mri_volsynth as you have below but add --delta-crsf C R S 0
where C, R, S are the col, row, slice from the voxel you found in freeview
On 9/9/2020 5:39 PM, Nasiriavanaki, Zahra wrote:
Hi
I am trying to make a subcortical 5 mm sphere ROI around a talairach
coordinate. I am using the below command, but when I visualize it, it
doesn’t look at the correct location. I see the same question in forum
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67295.html),
I should probably use -pdf delta but I don’t know how to get the col,
row and slice indices of the vertex where it should go.
mri_volsynth --template $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz
--c_ras -21.8 -12.2 -10.3 --dim 5 5 5 5 —o new.mgh
I appreciate your help.
Thanks
Mona
*Zahra (Mona) Nasiriavanaki, M.D.*
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
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