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 <dgr...@mgh.harvard.edu
<mailto:dgr...@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
<dgr...@mgh.harvard.edu <mailto:dgr...@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-boun...@nmr.mgh.harvard.edu<freesurfer-boun...@nmr.mgh.harvard.edu>on
behalf of Douglas N. Greve<dgr...@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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