There are a few comparisons. A recent paper by Liu et al. compares TORTOISE, DTIprep and DTI Studio:
Comparison of quality control software tools for diffusion tensor imaging
[
www.sciencedirect.com]
Another discussion has been made by AFNI user extraordinaire, Peter Molfese:
[
blog.cogneurostats.com]
I've worked on a bit of comparisons, as well, but am still waiting for reviewers to finish reading...
Do you have AP-PA data? That is, data acquired in two copies, with opposite phase encoding directions?
--pt
