Registration and warping of magnetic resonance images to histological sections

We present a method for coregistration and warping of magnetic resonance im ages (MRI) to histological sections for comparison purposes. This methodolo gy consists of a modified head and hat surface-based registration algorithm followed by a new automated warping approach using nonlinear thin plate sp lines to compensate for distortions between the data sets. To test the meth odology, 15 male Wistar rats were subjected to focal cerebral ischemia via permanent occlusion of the middle cerebral artery. The MRI images were acqu ired in separate groups of animals at 16-24 h (n=9) and 48-168 h (n=6) post occlusion, After imaging, animals were immediately sacrificed and hematoxyl in- and eosin-stained brain sections were obtained for histological analysi s. The MRI was coregistered and warped to histological sections. The MRI le sion areas were defined using the Eigenimage (EI) filter technique. The EI is a linear filter that maximizes the projection of a desired tissue (ische mic tissue) while it minimizes the projection of undesired tissues (nonisch emic tissue) onto a composite image called an EI. When using coregistration without warping the MRI lesion area demonstrated poor correlation (r=0.55, p>0.01) with a percent difference between the two lesion areas of 22.5%+/- 10.8%. After warping, the MRI and histology had significant correlation (r= 0.97, p<0.01) and a decreased percent difference of 5.56%+/-4.31%. This met hodology is simple and robust for coregistration and warping of MRI to hist ological sections and can be utilized in many applications for comparison o f MRI to histological data. (C) 1999 American Association of Physicists in Medicine. [S0094-2405(99)00908-6].