Do you mean your control and experimental groups have different acquisition protocols? In that case, this may compromise comparability between groups depending on the specific scientific question you are trying to answer. It would be helpful to know more details for a better answer.

Usually diagnostic MRI slices are taken at about 2mm or below. If isotropic voxel is employed, it is the best to use 1mm slice size. Small size slices give one assurance of diagnostic accuracy even at small lesions.

Saying this, I advise to use identical parameters for research unless comparison is deemed to b valuable.

Thanks