From Human MRI to Microscopy: Co-registration of Human Brain Images to Postmortem Histological Sections

Small vascular lesions seen in human MRI are detected reliably only in postmortem histological samples. Using non-linear polynomial transformation, we report a method to co-register in-vivo MRIs to microscopic examinations of histological samples drawn off the postmortem brain. Digital photographs of postmortem slices served as an intermediate reference to coregister the MRIs to microscopy. In-vivo MRI to postmortem coregistration is challenging due to gross structural deformations in the brain during extraction. Hemispheres of the brain were co-registered separately to mitigate these effects. Approaches relying on matching single-slices, multiple-slices and entire volume in conjunction with different similarity measures suggested that using four slices at a time in combination with two sequential measures, Pearson correlation coefficient followed by mutual information produced the best MRI-postmortem coregistration according to a voxel mismatch count. The accuracy of the overall registration was evaluated by measuring the 3D Euclidean distance between the locations of the microscopically identified vascular lesions and their MRI-postmortem coregistered locations. The results show a mean 3D displacement of 7.5 plusmn 2.7 mm between these locations for 11 vascular lesions in 7 subjects.