I'm glad you were able to get it working for you. Well, I had to look up these indices (Cl, Cp, Cs) to find out what they mean. For anyone who may be interested, they are defined in this paper by Westin, et al, [
lmi.bwh.harvard.edu] Essentially, these are alternative anisotropy indices comparing the relative eigenvalues, easily calculable with 3dcalc.
Similar maps are also done with FA (fractional anisotropy) > than some threshold say about 0.25 and using the eigenvectors themselves as the R,G,B components. This command prepares the FA scaled primary eigenvector and the RGB dataset
3dcalc -prefix DTieva00rw -a 'DTi00+orig.[9..11]' -c 'DTi00+orig.[18]' -expr 'c*STEP(c-0.25)*255*ABS(a)'
3dThreetoRGB -prefix DTiRGB00rw -anat 'DTieva00rw+orig.[0]' 'DTieva00rw+orig.[1]' 'DTieva00rw+orig.[2]'
Here, voxels with FA less than 0.25 are not displayed. I'd be interested to see how they compare with the Cl, Cp RGB image.
