Opening FA color map created by MRtrix in other software

Hi everyone,

We have calculated the FA (colored) map with dwi2tensor and tensor2metric. However, when opening it with other viewers for .nii files, such as MRIcro, it is a greyscale image. It looks like the vector information is saved in layers and only MRview can visualize it as a color map (there it looks normal). Also, Trackvis is unable to open the file (unknown error). How can we solve this?

Many thanks in advance!


Hi Klara,

Directionally-encoded colour (DEC) data are stored as 4D images with three volumes; the non-negative values in each of these volumes correspond to the red, green and blue components of the colour / intensity of each voxel. This should be evident in the output of mrinfo.

Assuming the data have been generated correctly, which should be the case if mrview shows it correctly, I can think of two things that may conceivably lead to issues:

  • Other softwares may require that the values stored within a DEC image lie within the range [0, 1], and fail to display as such / produce an error if this is not the case. FA values may exceed 1 in the presence of negative eigenvalues. You could try running mrstats on the image, and check the minimum / maximum values.

  • I was going to suggest that other softwares may have been expecting a NIfTI Intent Code to display a DEC image; but there doesn’t actually appear to be an intent code for such…

In MRIcro, is it a greyscale FA image that is shown, or the first volume of the image (i.e. the left-right component of the first eigenvector, scaled by FA)? You can visualise the latter in mrview by changing the colour map from RGB to greyscale.