It looks to me that the orientations of your VASO datasets is not correct. With this partial data, it's hard to say what is correct, but the orientation might be LPS. You can reset that with 3drefit -orient LPS (better on a copy of the data, of course). Still, that might not be enough to solve this problem.Using affine transformations across software packages can be problematic because of differences in definitions. With lost information from the header, that can be very difficult to solve. You may want to stick with one software package all the way through transformations.