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Registration

Registration refers to the process of aligning images together, and is a fundamental step in all MRI image analysis tasks. FSL contains a selection of high quality image registration tools, which can be used to linearly and non-linearly align two images together.

Most registration tasks begin with calculating a set of global translations, scalings, and rotations - this is referred to as a linear registration, and can be performed using FLIRT. Once two images are roughly aligned, it is common to calculate a non-linear registration to achieve fine-grained alignment of anatomy. Both FNIRT and its successor MMORF are high-performance and robust non-linear registration tools.

FSL also includwes MSM, which implements an alternative surface-based registration framework, and is a core component of the Human Connectome Project (HCP) processing pipeline.