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 10, 2020, at 5:36 PM, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
Try using --pdf sphere --sphere-center 150 138 116 --radius 5
instead of delta

On 9/10/2020 2:22 PM, Nasiriavanaki, Zahra wrote:
thanks for you reply.
So, how should I define the size of the sphere around that coordinate?

I am trying to make a subcortical 5 mm sphere ROI around that talairach coordinate.

Thanks
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 10, 2020, at 1:18 PM, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
remove --dim 5 5 5 5
this tells it to make the output volume 5 voxels

On 9/10/2020 12:53 PM, Nasiriavanaki, Zahra wrote:
Sure, sorry for the inconvenience.
Here is the full output:

[bee:ROI_analysis] (nmr-stable6-env) ./make_flabels.sh

volid delta.mgh

volfmt (null)

Using /autofs/space/oprah_001/users/zn025/looming_3T/SUBJECTS_DIR/fsaverage/mri/brainmask.mgz as template

fwhm = 0, gstd = 0

seed 1600286417

pdf delta

SpikeTP -1

DoCurv 0

DoAbs 0

Diagnostic Level -1

INFO: reading template header

Synthesizing

delta set to 1 at 150 138 116 0

./make_flabels.sh: line 43: 20329 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
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 10, 2020, at 12:39 PM, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
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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