IPT imfuse() is not an image compositing tool. It's a simple tool for visually comparing two images. This is why everything is turning inconsistent shades of green:
The answer is to not use imfuse(). Identify which image (if any) is to be the background, and create masks from the others. Then compose the output image based on those masks and whatever feature colors you want. I'm going to make some assumptions for the sake of example, but this should be a start.
% read the images
% i'm assuming these are already the same size
% i don't know where you're getting the trajectory image
% i just created this one from the screenshot
fullmap = imread('fullmap.png'); % 600x600 RGB uint8
fastpath = imread('fastpath.png'); % 600x600 RGB uint8
tjmask = imread('trajectory.png'); % 600x600 I logical
% convert fastpath to a simple grayscale mask
% if the trajectory image is also RGB, do similar to it.
fpmask = imadjust(im2gray(fastpath));
% pick your colors
fpcolor = [0 1 0];
tjcolor = [0.5 0 0];
% compose the output
% this is how i'd do it in MIMT, safe and class/depth agnostic
%outpict = replacepixels(fpcolor,fullmap,fpmask);
%outpict = replacepixels(tjcolor,outpict,tjmask);
% this mess is how it's done in IPT
fpmask = im2double(fpmask);
tjmask = im2double(tjmask);
outpict = fpmask.*permute(fpcolor,[1 3 2]) + (1-fpmask).*im2double(fullmap);
outpict = tjmask.*permute(tjcolor,[1 3 2]) + (1-tjmask).*im2double(outpict);
outpict = im2uint8(outpict); % presume the output class
% show the output
imshow(outpict,'border','tight')
