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. >
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