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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Wednesday, September 9, 2020 6:23 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto: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<mailto: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<mailto: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
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