Fig. 7

Overview of MRI-histology co-registration approach. a Photograph of tissue block (block face). b Photograph of coronal brain slice after the excision of tissue blocks. c Photograph of intact coronal brain slice. d Same as a after removing the blue background. e Same as c after removing the blue background. f Photograph of intact brain slice with inserted block face. Block insertion is a rigid-body registration that uses normalised mutual information (NMI [58]) as a cost function. The histology image will, later on, be transformed to fit the region of interest defined by this block. g Histology image that is registered to the block face using non-linear, deformable registration (cost function: MIND [106]). h Slice of the MR volume that was re-sampled along a curvilinear surface to represent the anatomical features of e. i Tissue-type segmentation of e. The boundary between white matter and grey matter is registered to the same boundary in h using boundary-based registration (cost function: BBR [108]). j Final alignment of the histology to the resampled MR volume (only one slice is shown)