I used fsl2ascii to convert my .nii files to ascii.txt files with the raw FA information and opening/manipulating the text files is straightforward in R and Matlab. Another tools you can use is nibabel (python) and oro nifti (R).

Also, try https://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image.

Regards,
Faizan