First, use -cifti-math to do the thresholding you want (if you have negative p-values for deactivations, you could add something like " + 2 * ((x < 0) && (x > -0.05))"):
$ wb_command -cifti-math '(x > 0) && (x < 0.05)' above_thresh.dscalar.nii -var x <your p-statistic file here> Then, import it as a label file (this basic version will give a random color and the name "LABEL_1", read the command help for how to assign colors and names): $ wb_command -cifti-label-import above_thresh.dscalar.nii "" above_thresh.dlabel.nii Then when displaying this file on top of something (we recommend a beta map), you can click the wrench for the dlabel layer, go to the "Labels" tab, and change the drawing type from "filled" to "outline color" or "outline label color". Tim On Mon, Nov 27, 2017 at 6:24 PM, Xavier Guell Paradis <[email protected]> wrote: > Thank you very much for your reply. > I have a map of surface cerebral cortical p values in a dscalar file, and > would like to create a dlabel file corresponding to the values between 0 > and 0.05 so that I can display this as an outline. > I have not been successful when trying to create this dlabel file from my > dscalar file using wb_command. Is there a succession of commands that you > would recommend to achieve this? > > Thank you very much for your help, > Xavier. > ------------------------------ > *From:* Glasser, Matthew [[email protected]] > *Sent:* Monday, November 27, 2017 4:01 PM > *To:* Xavier Guell Paradis; [email protected] > *Subject:* Re: [HCP-Users] Show outline of dscalar map at a given > threshold? > > You can create a .dlabel.nii of the above threshold vertices and then > display this as an outline. There isn’t a way of doing this directly on a > .dscalar.nii. > > Peace, > > Matt. > > From: <[email protected]> on behalf of Xavier Guell > Paradis <[email protected]> > Date: Monday, November 27, 2017 at 2:29 PM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] Show outline of dscalar map at a given threshold? > > Dear HCP experts, > I was wondering if there is a way to show the outline of a dscalar map at > a given threshold in workbench view. For example, I may have dscalar file > with z values for the cerebral cortical surface, and may want to show only > the outline of clusters corresponding to z>4 in that dscalar file. > I have been exploring the options in workbench view and the mail archive > and could not find a way to do this. I thought of playing with the > thresholds (e.g. low threshold=4, high threshold=4.5, show data inside > thresholds), but of course this only generates an ugly, uneven outline of > the z>4 clusters. > > Thank you very much, > Xavier. > > _______________________________________________ > 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
