Hi Cristian –
How are you generating your .nii files in the first place? Do you have corresponding bvec and bval files already?
I don’t think we have a tool available from our site for doing this, but if you have FSL installed I believe you can do it with that. Let me know about the bvec/bval files, and I will see how we can help you with this.
thanks,
David Shattuck