A template for spatial normalisation of MR images of the rat brain

In this paper, we describe the preparation of a rat template intended for use together with SPM to enable spatial normalisation of individual rat brains. The template was created from T2-weighted images of the brains of five adult female Sprague-Dawley rats. A large number of anatomical landmarks were manually identified in each of these image volumes and recorded in the appurtenant image space. The same landmarks were defined in the space of the commonly used atlas by Paxinos and Watson. For each individual volume the affine transformation that best (in a least square sense) matched the two sets of points was estimated. These transforms were used to resample the individual volumes into the "Paxinos space", and a template was created from the average of these. Hence, a rat brain spatially normalised to this template will facilitate reporting results in co-ordinates directly corresponding to the Paxinos co-ordinate system. The usage of the template is exemplified with a functional magnetic resonance imaging (fMRI) study of the somatosensory cortex of the rat. The template image volumes together with the necessary modifications to the SPM software code can be downloaded from http://mr.imaging-ks.nu/expmr.htm.