Hi James and Martin  I had a similar problem than James converting nrrd files to FSL. Using the latest version of DWIConvert and flag ---outputNiftiFile instead of--outputVolume in Slicer 4.8, it wirtes bvec file with gradients directions exactly as in nifti. However this works with standard nrrd files, but not for preprocessed DTIPrep nrrd files (*_QCed.nrrd). It reports that the only supported output is "short" . There is an "unsigned short" in the headers of *QCed.nrrd instead of "short" in the regular nrrd files.
 Any suggestions of how to solve this would be very appreciated.

I am attaching an example of this QCed.nrrd file in case it helps

Thanks