A ranking of pipelines for optimal co-registration of anatomical and diffusion weighted images of the cervical spinal cord

We conduct the first systematic evaluation of the performance of three widely used registration software toolkits (FLIRT from FSL, NiftyReg and ANTs employing Spinal Cord Toolbox) in an effort to outline a method for reliable co-registration between anatomical and quantitative (EPI-based) spinal cord MRI. We generate a diverse set of registration pipelines and rank them according to quality of co-registration metrics. We find that ANTs and NiftyReg outperform FLIRT, and we report heterogeneity of specifications for optimal co-registration among software toolkits.