OK, it's more clear. But how / why this should create accurately circular patches? I just get patches as before -or I do not call it correctly. Also, unfortunately, from the help it is not clear to me what dilate function tries to achieve... Thanks again.
On Wed, Apr 26, 2017 at 9:53 PM, Glasser, Matthew <[email protected]> wrote: > Given your output of wb_command -surface-geodesic-distance is a metric > GIFTI file you could use -metric-dilate. > > Peace, > > Matt. > > From: Vadim Axel <[email protected]> > Date: Wednesday, April 26, 2017 at 1:40 PM > To: Matt Glasser <[email protected]> > Cc: "Elam, Jennifer" <[email protected]>, "[email protected]" < > [email protected]>, "Dierker, Donna" <[email protected]> > > Subject: Re: [HCP-Users] automatic drawing of circles on a surface > > Thank you, Matt. But can you please provide more details because I do not > fully understand. There are -cifti-dilate, -metric-dilate and > -label-dilate. Which one do I use? If this is the former, it seems that I > still need to create the label manually. If you mean two former, it is not > clear to me how I "start with values at the vertices". > > On Wed, Apr 26, 2017 at 8:50 PM, Glasser, Matthew <[email protected]> > wrote: > >> You should be able to start with values at the vertices and then use a >> dilate command to make the circles. >> >> Peace, >> >> Matt. >> >> From: <[email protected]> on behalf of Vadim Axel < >> [email protected]> >> Date: Wednesday, April 26, 2017 at 12:46 PM >> To: "Elam, Jennifer" <[email protected]> >> Cc: "[email protected]" <[email protected]>, >> "Dierker, Donna" <[email protected]> >> >> Subject: Re: [HCP-Users] automatic drawing of circles on a surface >> >> 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. 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If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> > > > ------------------------------ > > 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
