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.
Procedure:
- Used
reg_aladin
for affine registration of the CEST image to the T1c. - Saved the transformation matrix to a .txt file.
- 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?