Last question: why should it be different from the output of -surface-geodesic-distance?
On Wed, Apr 26, 2017 at 10:15 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > If you start from a single point and dilate the patches should be > approximately circular. > > Peace, > > Matt. > > From: Vadim Axel <axel.va...@gmail.com> > Date: Wednesday, April 26, 2017 at 2:13 PM > > To: Matt Glasser <glass...@wustl.edu> > Cc: "Elam, Jennifer" <e...@wustl.edu>, "hcp-users@humanconnectome.org" < > hcp-users@humanconnectome.org>, "Dierker, Donna" <do...@wustl.edu> > Subject: Re: [HCP-Users] automatic drawing of circles on a surface > > 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 <glass...@wustl.edu> > 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 <axel.va...@gmail.com> >> Date: Wednesday, April 26, 2017 at 1:40 PM >> To: Matt Glasser <glass...@wustl.edu> >> Cc: "Elam, Jennifer" <e...@wustl.edu>, "hcp-users@humanconnectome.org" < >> hcp-users@humanconnectome.org>, "Dierker, Donna" <do...@wustl.edu> >> >> 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 <glass...@wustl.edu> >> 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: <hcp-users-boun...@humanconnectome.org> on behalf of Vadim Axel < >>> axel.va...@gmail.com> >>> Date: Wednesday, April 26, 2017 at 12:46 PM >>> To: "Elam, Jennifer" <e...@wustl.edu> >>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>, >>> "Dierker, Donna" <do...@wustl.edu> >>> >>> 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 <e...@wustl.edu> 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 >>>> e...@wustl.edu >>>> 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> >>>> 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 <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 >>>>> 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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