Automated longitudinal registration of high resolution structural MRI brain sub-volumes in non-human primates

Accurate anatomic co-registration is a prerequisite for identifying structural and functional changes in longitudinal studies of brain plasticity. Current MRI methods permit collection of brain images across multiple scales, ranging from whole brain at relatively low resolution (≥1 mm), to local brain areas at the level of cortical layers and columns (∼100 μm) in the same session, allowing detection of subtle structural changes on a similar spatial scale. To measure these changes reliably, high resolution structural and functional images of local brain regions must be registered accurately across imaging sessions. The present study describes a robust fully automated strategy for the registration of high resolution structural images of brain sub-volumes to lower resolution whole brain images collected within a session, and the registration of partially overlapping high resolution MRI sub-volumes (“slabs”) across imaging sessions. In high field (9.4 T) reduced field-of-view high resolution structural imaging studies using a surface coil in an anesthetized non-human primate model, this fully automated coregistration pipeline was robust in the face of significant inhomogeneities in image intensity and tissue contrast arising from the spatially inhomogeneous transmit and receive properties of the surface coil, achieving a registration accuracy of 30 ± 15 μm between sessions.

► Investigation of structural and functional remodeling of the brain requires accurate registration.
► Surface coils permit the acquisition of very high resolution slabs but the position of the coil changes between sessions and causes problems.
► Partial overlap and rapidly dropping signal make the direct registration extremely challenging.
► Proposition of an automated method to register slab based on intermediate image.
► Proof of the method on squirrel monkey with accuracy of 30 ± 15 μm.