You should also consider the command -surface-geodesic-rois, which will act similar to a manual dilation of single vertex maps, but takes input as a text file, like -surface-closest-vertex generates:
http://www.humanconnectome.org/software/workbench-command.php?function=-surface-geodesic-rois Part of the issue you are getting, though, is that your chosen distance threshold is very close to the 32k vertex spacing, and thus it won't even reliably get the hexagon of immediate neighbors. Dilation actually has a workaround for this, in that with small dilation amounts, it dilates by a minimum of one vertex. A better solution for cleaner circles would be to use the 164K surface. However, if you aren't looking for patches of vertices that could be used for processing, but instead just symbols for visualization, foci is indeed closer to what you want. Unfortunately, wb_command doesn't have a command to create foci files, as they are somewhat of a legacy format. There might be something in caret5 for this. Tim On Wed, Apr 26, 2017 at 2:24 PM, Glasser, Matthew <[email protected]> wrote: > That is a map of distances. You could threshold this at something, > binarize it, and then dilate. > > Peace, > > Matt. > > From: Vadim Axel <[email protected]> > Date: Wednesday, April 26, 2017 at 2:20 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 > > 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 <[email protected]> > wrote: > >> If you start from a single point and dilate the patches should be >> approximately circular. >> >> Peace, >> >> Matt. >> >> From: Vadim Axel <[email protected]> >> Date: Wednesday, April 26, 2017 at 2:13 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 >> >> 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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