Dear FSL Users,
I am trying to use overlay followed by slicer to create a png containing a montage of axial images. First, I use overlay to superimpose an activation map on a structural template:
overlay 1 0 trh40002-0019 -a trh40002-0019reg5bin 0 1 output
this works fine and when I view output.nii.gz in fslview or DTI-TK quick look plugin it looks as expected. However, when I try to use slicer to create the desired montage, my background anatomical image comes out red and my activation regions (which, by the way, are binary) are yellow.
I use the following inputs to overlap:
slicer output -A 1250 coronal_images.png
Any thoughts on how to remove the color from coronal_images.png and instead just generate a greyscale .png would be most appreciated!
Best,
Marc
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