MMORF—FSL’s MultiMOdal Registration Framework

Abstract We present MMORF—FSL’s MultiMOdal Registration Framework—a newly released nonlinear image registration tool designed primarily for application to magnetic resonance imaging (MRI) images of the brain. MMORF is capable of simultaneously optimising both displacement and rotational transformations within a single registration framework by leveraging rich information from multiple scalar and tensor modalities. The regularisation employed in MMORF promotes local rigidity in the deformation, and we have previously demonstrated how this effectively controls both shape and size distortion, leading to more biologically plausible warps. The performance of MMORF is benchmarked against three established nonlinear registration methods—FNIRT, ANTs, and DR-TAMAS—across four domains: FreeSurfer label overlap, diffusion tensor imaging (DTI) similarity, task-fMRI cluster mass, and distortion. The evaluation is based on 100 unrelated subjects from the Human Connectome Project (HCP) dataset registered to the Oxford-MultiModal-1 (OMM-1) multimodal template via either the T1w contrast alone or in combination with a DTI/DTI-derived contrast. Results show that MMORF is the most consistently high-performing method across all domains—both in terms of accuracy and levels of distortion. MMORF is available as part of FSL, and its inputs and outputs are fully compatible with existing workflows. We believe that MMORF will be a valuable tool for the neuroimaging community, regardless of the domain of any downstream analysis, providing state-of-the-art registration performance that integrates into the rich and widely adopted suite of analysis tools in FSL.