I found the answer to my question. 
Thanks anyway


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 6:06 PM, Nasiriavanaki, Zahra <ZNASIRIAVANAKI@mgh.harvard.edu> wrote:

Thanks for your reply.
So I did these steps to get the values from the spherical ROI that I created and got the below error:

mri_volsynth --template $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --pdf sphere --sphere-center 150 138 116 --radius 5  --o /autofs/space/oprah_001/users/zn025/looming_3T/SUBJECTS_DIR/ROI/sphere/lhamyg.mgh
mri_binarize --i /autofs/space/oprah_001/users/zn025/looming_3T/SUBJECTS_DIR/ROI/sphere/lhamyg.mgh --min 10e-5 --o /autofs/space/oprah_001/users/zn025/looming_3T/SUBJECTS_DIR/ROI/sphere/lhamyg.bin.mgh
mri_segstats --seg /autofs/space/oprah_001/users/zn025/looming_3T/SUBJECTS_DIR/ROI/sphere/lhamyg.bin.mgh --id 1 --i /autofs/space/oprah_001/users/zn025/looming_3T/group_levels/Feb2020/combined_84/loom.mni/aw/ces.mgh --avgwf y.delta.sm5.bin.dat

ERROR:

dev
cwd 
cmdline mri_segstats --seg /autofs/space/oprah_001/users/zn025/looming_3T/SUBJECTS_DIR/ROI/sphere/lhamyg.bin.mgh --id 1 --i /autofs/space/oprah_001/users/zn025/looming_3T/group_levels/Feb2020/combined_84/loom.mni/aw/ces.mgh --avgwf y.delta.sm5.bin.dat 
sysname  Linux
machine  x86_64
user     zn025
whitesurfname  white
UseRobust  0
Loading /autofs/space/oprah_001/users/zn025/looming_3T/SUBJECTS_DIR/ROI/sphere/lhamyg.bin.mgh
Loading /autofs/space/oprah_001/users/zn025/looming_3T/group_levels/Feb2020/combined_84/loom.mni/aw/ces.mgh
ERROR: dimension mismatch between input volume and seg
  input 76 76 93
  seg   256 256 256





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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