Hi, Maksym-
DR-BUDDI questions should be directed to the TORTOISE folks, but I will have a go at this one:
Yes, the blipup and blipdown sets need to: have the same number of volumes, be acquired with the same grads, and be in the same order. And yes, the order of the rows in the bmatrix text file must correspond to the order of the volumes in the NIFTI dsets.
--pt