Change colored FA map and tractography results

Hi experts,
I used the following command lines to generate a colored FA map, which contains red, green and blue components, corresponding to the intensity within each voxel.

dwi2tensor dwi.mif tensor.mif
tensor2metric tensor.mif -vec dec.mif

However, this RGB color scheme might not be friendly for the color-blinded readers. Is it possible to change another color scheme in MRtrix? Similarly, tck. file contains fiber tracking result, which also uses RGB to encode the orientation of fiber tracts. Is it also possible to change another color scheme to visualize the orientation of fiber tracts? Thanks again for your help.


Hi @wscain,

I’m not aware of any work in this area. The main reference for the colour schemes we currently use dates back to 1999, and I haven’t seen anything about the matter since, that I can remember…

Yes, though it would require changes in the code. But more importantly, it would require an appropriate replacement strategy. I can’t think of a simple fix here: the advantage of the RGB scheme is that it has 3 channels, which can be used to map to the 3 XYZ components. My understanding of colour blindness is that the R&G (typically) merge into one, meaning that we effectively only have 2 channels that can be used. While it may be theoretically possible to map azimuth & elevation angles onto 2 channels, I can’t see how it can be done without discontinuities – but there may be some clever trick I’m missing…

In any case, if you have ideas you’d like to try, the simplest is to convert an RGB image (e.g. the DEC-FA) to a different scheme, but still represented as RGB, which you can then trivially display in mrview. If that proves successful, you could try to implement that for the streamlines rendering too, but at that point you’ll be modifying OpenGL shaders (these lines in particular)…

All the best,