I did it, and here is what I get for one of the images:
data type: sint16
position: -87.5 -119.715 -140.245
file orientation: identity matrix (3×3)
working orientation : identity matrix (3×3)
I compared with one of the images provided by Brainsuite for training, and the only differences are the data type and the file orientation (the first term is -1 in the provided example’s matrix instead of 1). Could the problem come from here? Is it fixable?