[Freesurfer] interchanging between FSL freesurfer

Hi, my name is Martina and I'm a student of biomedical engineering in Rome. I'm doin g a brain imaging research for my final exam. I'm using freesurfer for registration and segmentation of brain images instead o f FSL tools (flirt,bet and fast) and then continue to process the data with FSL. But I have a problem: after converting the image generated with freesurfer mri_ convert to ".nii" format it does not overlap with FSL's reference MNI152. I know that freesurfer uses talairach reference. Is it true? May it be the problem? How can I superimpose properly the images? Do you know any workaround? Thank you very much. Regards Martina Andellini