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
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
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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, September 9, 2020 6:23 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 mailto: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.edufreesurfer-bounces@nmr.mgh.harvard.eduon behalf of Douglas N. Grevedgreve@mgh.harvard.edu *Sent:*Wednesday, September 9, 2020 6:23 PM *To:*freesurfer@nmr.mgh.harvard.edufreesurfer@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 mailto: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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
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.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, September 9, 2020 6:23 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 mailto: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 mailto: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.edufreesurfer-bounces@nmr.mgh.harvard.eduon behalf of Douglas N. Grevedgreve@mgh.harvard.edu *Sent:*Wednesday, September 9, 2020 6:23 PM *To:*freesurfer@nmr.mgh.harvard.edufreesurfer@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 mailto: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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
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 hostname bee.nmr.mgh.harvard.eduhttp://bee.nmr.mgh.harvard.edu 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.edumailto: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.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, September 9, 2020 6:23 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.edumailto: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 hostname bee.nmr.mgh.harvard.eduhttp://bee.nmr.mgh.harvard.edu/ 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.edumailto: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.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, September 9, 2020 6:23 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Nasiriavanaki, Zahra