Hi Doug

Thanks for your reply.

I did so, I'm getting the error below:

line 43:  8101 Segmentation fault      (core dumped) mri_volsynth --template $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --c_ras -21.8 -12.2 -10.3 --pdf delta --delta-crsf 150 138 116 0 --dim 5 5 5 5 --o delta.mgh

I appreciate your help.

Thanks

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129

---

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Wednesday, September 9, 2020 6:23 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_volsynth question

 

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

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

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