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Hi Siewmin (and I guess this should answer Sid's questions as well), If you run FSL's eddy_correct on your data, then this will, as you know, produce a text file called blah.ecclog You can then use the attached matlab script which will read your ecclog file and bvecs file, and apply the appropriate rotations to your bvecs. The top-left 3x3 of the flirt matrices do not only contain rotations, so you need to do a little trick to extract the rotation part (this is done for you in the matlab script attached). In my experience, I did not notice a huge difference in my data when comparing e.g. FA before and after bvecs rotation, but I guess it might make a difference on other data... The relation between the amount of bvecs rotation and the output of dtifit and/or the end result of tractography is not straightforward, so I am not sure you can objectively assess whether a correction for the bvecs rotation is necessary or not just by looking at MCFLIRT results. Cheers, Saad.