Nice feature, thanks Jennifer. Though, not sure that it will help me because I have hundreds of patches that should be created automatically. As far as I understand, there is no functionality to create foci file automatically.
BTW, unrelated, I wonder whether there is a way in the workbench to select some vertex not by a mouse click, but by providing the vertexID (or MNI coordinate). Something like in matlab Ctrl+G, where you jump directly to some line. Thank you. On Wed, Apr 26, 2017 at 6:31 PM, Elam, Jennifer <[email protected]> wrote: > 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 > [email protected] > www.humanconnectome.org > > ------------------------------ > *From:* [email protected] < > [email protected]> on behalf of Vadim Axel < > [email protected]> > *Sent:* Wednesday, April 26, 2017 9:41:23 AM > *To:* Dierker, Donna > *Cc:* [email protected] > *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 <[email protected]> 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 >> >> >> >> On Apr 26, 2017, at 5:17 AM, Vadim Axel <[email protected]> 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 >> [email protected] >> 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 > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
