Hi Vadim, You could also try creating foci at the coordinates of the electrodes in the wb_view GUI, which you could show as spheres like in the image you are trying to emulate.
To create foci, click on "Foci" in the Mode section of the Toolbar and a set of Foci buttons will appear at the bottom of the Toolbar. Click on "New" and use the dialog to create a *.foci file to save your foci, and add your first focus at your electrode coordinates, and make sure the "Project to Surface" checkbox is checked at the bottom of the dialog. Continue the process for all the electrodes you want to show. When you are done adding foci to the *.foci file you created, don't forget to go to File>Save/Manage Files to save the *.foci file to disk. Even though you set a file name in workbench, that doesn't save the file without this step. To adjust the way the foci are shown (size, shape, color, etc.), open the Features Toolbox (View>Features Toolbox, or toolbox-looking icon at the top far right). You also might want to create a *.scene file to save your work as you do this (clapboard icon at top right) so you can pick up where you left off if you need to, but again you need to go to File>Save/Manage Files to save the *.scene file to disk. There is Help info on all these features in the Workbench Help (? icon at top). Hope that helps! Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387<tel:314-362-9387> e...@wustl.edu<mailto:e...@wustl.edu> www.humanconnectome.org<http://www.humanconnectome.org/> ________________________________ From: hcp-users-boun...@humanconnectome.org <hcp-users-boun...@humanconnectome.org> on behalf of Vadim Axel <axel.va...@gmail.com> Sent: Wednesday, April 26, 2017 9:41:23 AM To: Dierker, Donna Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] automatic drawing of circles on a surface Thank you Donna. You are right that using midthickness my patches become more circular (though still not fully). However, the main reason I want to use the inflated or even very inflated view is because using for example midthickness some of the patches are hidden within the sulci (see attached image). The question is whether there is a way to make some drawing on the surface irrespective of vertices, probably by exporting the surface... On Wed, Apr 26, 2017 at 4:26 PM, Dierker, Donna <do...@wustl.edu<mailto:do...@wustl.edu>> wrote: Hi Vadim, Try looking at your patches on an anatomical surface (e.g., white, midthickness, pial). They probably will look more like what you expect. The inflated surface necessarily distorts the shape of overlays. See attached capture which shows distance borders from AVM on midthickness in the lower left corner, on the inflated at right. Donna [https://outlook.office.com/owa/?realm=email.wustl.edu&retryCount=2] On Apr 26, 2017, at 5:17 AM, Vadim Axel <axel.va...@gmail.com<mailto:axel.va...@gmail.com>> wrote: Dear experts, I use connectome workbench to visualize position of intracranial electrodes.My intention was to make a small circle around each location. For that, I took MNI coordinate of an ellectrode converted it to vertexID (wb_command -surface-closest-vertex) and then found vertices within 2mm (wb_command -surface-geodesic-distance). Instead of circles, I got non-circular patches (see attachment, left). Can someone suggest how can I create circles like in the right picture? Thanks for the help, Vadim _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users <sample.png> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
