Next, FNIRT is used to non-linearly register the aligned source image to the reference image. Importantly, both of these steps are performed using FSL coordinates. Note that we have three spaces, and three sets of coordinate systems, to consider: 1. Source image space - the source image, before initial linear registration to the reference image 2. Linear or affine registrations (eg FSL FLIRT) ¶ API link: regtricks.transforms.linear.Registration Registrations can be created from a np.array, a path to a text file that numpy can read, or by calling a wrapper for FLIRT. In all cases, the matrix should be 4x4 and the last row should be 0,0,0,1.