MRI Image Registration - Alignment Issues

Using NiftyReg for MRI Image Registration - Alignment Issues

I’ve used NiftyReg to align a series of CEST images (“amides”, “amines”, and “CEST”) to a T1 contrast-enhanced (T1c) image. My main reference image was cest_MPI03_APT-0002.nii due to its anatomical features.

Issue: Even though the primary CEST image registered well with the T1c reference, the “amides” and “amines” images were shifted upwards when I applied the same transformation matrix.


  1. Used reg_aladin for affine registration of the CEST image to the T1c.
  2. Saved the transformation matrix to a .txt file.
  3. Applied the transformation matrix to the “amides” and “amines” images with reg_resample.

Any insights on why there’s a misalignment and how to correct it?