Hi Rob,
Thank you for taking the time to answer. I eventually analyzed the data once again and got an identical error as the one here http://community.mrtrix.org/t/siemens-vs-philips-dwipreproc-eddy-error/1301/3 and it turned out that I also had poorly distributed directions, which is probably why eddy did not want to take it…I have since started using newer data with different acquisition parameters and I could run dwipreproc on it with no problems so far, luckily.
Best,
Sabina