Local volume changes of the corpus callosum from 3D MR images of wildtype and knockout mouse brains
Ghassan Hamarneh, Josette Chen, Nir Lifshitz, Mark Henkelman · 2003
We characterize 3D local volume changes of the corpus callosum from MR images of wildtype and neuro-transgenic fixed mouse brains. We demonstrate how the measurement technique could be used for detecting morphological phenotypes for mutant mouse screening. Methods We calculated local volume changes of wildtype and mutant mouse brain structures from the deformation field that maps the correspondence between structures. The deformation field encodes how each tri-ordinate (u,v,w) of a uniform lattice in the wildtype mouse image space is displaced to (U,V,W) in the mutant mouse image space. To establish this spatial correspondence for the wildtype and neuro-transgenic corpora callosa pair (denoted wCC and tCC, respectively), we segmented the wCC and tCC from the MR images (Figure 1a) using Livewire, a semi-automatic segmentation tool provided by Amira software (TGS, San Diego, CA). We then selected homologous wCCtCC landmarks (Figure 1b) and calculated a rigid transformation to align them (Figure 1c). We thereafter applied thin plate splines (TPS) interpolation to deform the wCC landmarks and surface to tCC (Figure 1d) as dictated by the new corresponding landmarks resulting from the rigid transformation (Figure 1c). The vertices (u,v,w) of a 3D uniform grid in the image space of wCC (Figure 1e) are also transformed using TPS into the new (a) (b) (c) warped grid (U,V,W) (Figure 1f). We then calculated the local volume change according to (see [1] for details):