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 <mailto: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
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