Registering different MRI modalities to sri24 atlas by FNIRT in FSL

I need to make isotropic voxels of MRI images by registering them to sri24 atlas before segmentation and radiomics. I registered the T1ce and FLAIR modalities with 156 and 240 slice numbers separately to the atlas with 155 slice numbers by FNIRT algorithm in FSL software (it was the only software that could handle different slice numbers), but the slices of registered images of T1ce and FLAIR did not match and were totally different.

I would really appreciate it if anyone could guide me to solve this problem.