Hi Russell,

Thanks a lot for your thorough response. I have a few other questions as well:

1) So, I used the "Tools for NIfTI and ANALYZE image" toolbox to look into the header and the header loaded into Matlab actually had three structures. I couldn't quite figure out which matrix you were mentioning when you were talking about the affine matrix and the fact that the image is in the RAS orientation.

2) Did you use glyphs to find out which orientation the gradient table was in after performing tractography?

I think I'll have more questions in a bit, but I'd appreciate if you can address these for now! :)

Thanks again and sorry for asking too many questions,
Ehsan