Proceedings IEEE Medical Imaging Conference, San Diego, Nov 2006 From Human MRI to Microscopy: Co-registration of Human Brain Images to Postmortem Histological Sections M. Singh, Senior Member, IEEE, A. Rajagopalan, C. Zarow, X.-L. Zhang, T.-S. Kim, D. Hwang, A.-Y. Lee, H. Chui Abstract– 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 co- register the MRIs to microscopy. In-vivo MRI to postmortem co- registration 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 co- registration 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 co- registered locations. The results show a mean 3D displacement of 7.5 ± 2.7 mm between these locations for 11 vascular lesions in 7 subjects. I. INTRODUCTION A microscopic examination of histological samples is often the gold-standard to detect pathology. For example, in diseases such as Alzheimer Disease or Vascular Dementia, small lesions may be visualized during in-vivo MRIs, but are detected reliably only at postmortem. With the objective of improving the detection and characterization of such small lesions seen in human MRIs but ascertained only at postmortem, we have developed a method to co-register MRI visualized lesions to those detected by a microscopic examination of histological samples drawn off the postmortem brain. The approach relies upon co-registration of digital photographs of the postmortem brain to the in-vivo MRI of the person when he or she was alive and mapping suspected lesions from the MRI to the corresponding postmortem slice. Manuscript received November 17, 2006. This work was supported in part by NIH Grants NIA-NIH 1PO1AG 12453 and NIA-NIH P50 AG05142. M. Singh. A. Rajagopalan, and D. Hwang are with the Departments of Radiology and Biomedical Engineering, University of Southern California, Los Angels, California, USA (Contact author e-mail: msingh@usc.edu). C. Zarow, X.-L. Zhang, A.-Y. Lee and H. Chui are with the Department of Neurology, University of Southern California, Los Angels, California, USA. T. S. Kim was with the Departments of Radiology and Biomedical Engineering, University of Southern California, Los Angels, California, USA. He is now with the Department of Biomedical Engineering, College of Electronics and Information, Kyung Hee University, Kyungki, South Korea. Relying on this image-guided procedure, samples are then drawn from a small region surrounding the location of mapped lesions in the postmortem slice, stained and examined microscopically to identify lesions. The locations of the microscopically detected lesions are marked on the histological samples. These marked samples are then co- registered back onto the postmortem slice. Thus the postmortem brain slices become the common frame-of- reference onto which the in-vivo MRI and the histological exam are mapped to achieve co-registration between MRI and microscopy. Previous work to co-register in-vivo MRIs to microscopically examined samples has been reported mostly for small animals [1-4], a limited number of primates [5] and relatively few human studies [6-8]. Animal studies have an advantage over human studies in that animals can be sacrificed immediately after an in-vivo scan, the postmortem brain can also be scanned, and then the postmortem brain can be frozen and sliced for a microscopic histological examination. Thus very little time elapses between the in- vivo, postmortem and microscopic examinations, thereby minimizing changes in the shape and structure of the brain viewed by the different modalities. Also, in animal studies it is logistically straightforward to obtain a scan of the premortem and postmortem brain. Thus a MRI of the postmortem brain is available to co-register with the microscopic examination. In human studies, however, frequently there is a large time- gap, on the order of 1-3 years, between the in-vivo MRIs and when the person comes to postmortem. Also logistically it is difficult to arrange for a MRI of the postmortem brain, and in the work reported here, no MRIs of the postmortem brain were available. Give these practical constraints, the objective of this work was to co-register in-vivo MRIs to digital photographs of postmortem slices and subsequent histological sections under the assumption that only in-vivo MRIs (which may have been done several years prior to death) are available, and that no postmortem MRIs would be available. Postmortem images in this paper specifically refer to digital photographs of the sliced postmortem brain and not any postmortem MRIs. Co-registering these photographs of the postmortem slices to corresponding in-vivo MR slices is a challenging task for a number of reasons: 1) The time lapse between the in-vivo MRI and the postmortem brain creates structural discrepancy, 2) the procedure to extract the brain from the cranial vault leads to multiple deformations such as collapse of the