please send the full terminal output
On 9/10/2020 11:24 AM, Nasiriavanaki, Zahra wrote:
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
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