Re: [Freesurfer] visualizing seeds on surface
If you know the vertex number, then you can do something like mri_volsynth --template $SUBJECTS_DIR/subject/surf/lh.thickness --pdf delta --delta-crsf vertexno 0 0 0 --o delta.mgz mris_fwhm --smooth-only --fwhm 5 --i delta.mgz --subject subject --hemi lh --o delta.sm05.mgz mri_binarize --i delta.sm05.mgz --min .1 --o delta.sm05.bin.mgz tksurferfv subject lh inflated -fminmax .5 1 -ov delta.sm05.bin.mgz This is a fairly convoluted method that basically creates a surface overlay with a 1.0 in your vertex and 0 everywhere else (delta.mgz), then smooths that to distribute non-zero values around the vertex, then binarizes it. On 05/02/2018 05:52 PM, Eryilmaz, H. Hamdi wrote: > Hi Doug, > > They are in MNI but I can find out their vertex numbers if that would > be easier. > > Thanks! > Hamdi > > > > *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, May 2, 2018 5:42:20 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] visualizing seeds on surface > What coordinate system are the seed coordinates in? Do you know the > vertex number on the surface? > > > On 05/02/2018 03:13 PM, Eryilmaz, H. Hamdi wrote: > > > > Dear freeview experts, > > > > Is it possible to display multiple seeds (i.e., as a small circle) on > > freeview surface view by specifying their coordinates? If there is no > > such feature, could you suggest an alternative way to visualize seeds? > > > > Thanks in advance! > > > > Best, > > Hamdi > > > > > > > > > > ___ > > 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 > 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] visualizing seeds on surface
Hi Doug, They are in MNI but I can find out their vertex numbers if that would be easier. Thanks! Hamdi 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, May 2, 2018 5:42:20 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] visualizing seeds on surface What coordinate system are the seed coordinates in? Do you know the vertex number on the surface? On 05/02/2018 03:13 PM, Eryilmaz, H. Hamdi wrote: > > Dear freeview experts, > > Is it possible to display multiple seeds (i.e., as a small circle) on > freeview surface view by specifying their coordinates? If there is no > such feature, could you suggest an alternative way to visualize seeds? > > Thanks in advance! > > Best, > Hamdi > > > > > ___ > 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 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] visualizing seeds on surface
What coordinate system are the seed coordinates in? Do you know the vertex number on the surface? On 05/02/2018 03:13 PM, Eryilmaz, H. Hamdi wrote: > > Dear freeview experts, > > Is it possible to display multiple seeds (i.e., as a small circle) on > freeview surface view by specifying their coordinates? If there is no > such feature, could you suggest an alternative way to visualize seeds? > > Thanks in advance! > > Best, > Hamdi > > > > > ___ > 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] visualizing seeds on surface
Dear freeview experts, Is it possible to display multiple seeds (i.e., as a small circle) on freeview surface view by specifying their coordinates? If there is no such feature, could you suggest an alternative way to visualize seeds? Thanks in advance! Best, Hamdi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
