External Email - Use Caution Got it, thanks!
Could you tell me how I can map a particular ROI (for instance the Destrieux cortical surface ROIs) to a set of vertices that make up the ROI? Is there a lookup table I can use? _______________________ Ben Smith, MSc. Ph.D. Candidate University of Southern California https://bjsmith.github.io/ p | +1 323-385 9349 skype | ben.smith.nz On Tue, Jul 10, 2018 at 2:08 PM Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> wrote: > Hi Ben, > > My last email was referring to how to load custom color map for volume > viewing. If you want to load custom color for surface, you need to create > and load an RGB map file. The file can be a text file contains N lines of > RGB color like this: > > R1, G1, B1 > R2, G2, B2 > > ... > > or a volume file with dimension of N x 3 x1. N must match the number of > vertices of the surface. > > Best, > Ruopeng > > On 07/10/2018 04:57 PM, Ben Smith wrote: > > External Email - Use Caution > I've been trying to do this as well, but I can't see the right place to > specify in freesurfer to specify an alternative lookup table. > > For instance, if I am coloring a pial surface, then the first possibility > is to set a Color (where I can "load RGB map"). But I get an error "Cannot > load RGB" file if I try to use that to load an LUT format file. The other > option is where it says "heatmap" i can change the option to select a > custom label, but if I try to enter an LUT file into there, freeview > crashes (which is fine, I guess that was the wrong place). > > So can anyone tell me what I'm missing for the place to load the LUT file > or an alternative colormap? > > Thanks for your help! > > Regards > > Ben > > On Tue, Mar 27, 2018 at 1:10 PM Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> > wrote: > >> It looks like a customized look up table will work for your case. You can >> simply select "Lookup table" as the colormap and load your own lookup >> table. To create your own look up table, you can refer to the content of >> FreeSurferColorLUT.txt file in your freesurfer installation directory. >> >> Best, >> Ruopeng >> On 03/27/2018 03:59 PM, Anna Mynick wrote: >> >> Hi all, >> >> I’m wondering whether there’s a way to create a custom color map in >> Freeview that would operate as a alternative to the preset Greyscale, >> Heatmap, NIH, PET, Jet and GE Color options. >> >> Ideally, I could assign each number value a given color, e.g. every “0” >> value in an .nii file is black, every “1” value is red, every “2” value is >> blue, every “3" is green and so on. I already have the RGB values worked >> out for each number value; I just need to know how to format this >> information and where to put it so that I can my custom colormap as an >> option in Freeview. >> >> For my purposes, there would be no need to adjust the assigned colors >> based on the overall range of values. For instance, there would be no need >> to assign a different color value to a “1” value depending on whether the >> highest value in the overall .nii file is 1 or 100. >> >> I did try reading the related conversation here >> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-April/051277.html> >> but >> I can’t seem to find the file it references, annotval2surfoverlay.m, in >> the Freesurfer directory. >> >> Thanks very much for your help! >> Anna >> >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
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