Comparison of Super Resolution Reconstruction Acquisition Geometries for Use in Mouse Phenotyping

3D isotropic imaging at high spatial resolution (30–100 microns) is important for comparing mouse phenotypes. 3D imaging at high spatial resolutions is limited by long acquisition times and is not possible in many in vivo settings. Super resolution reconstruction (SRR) is a postprocessing technique that has been proposed to improve spatial resolution in the slice-select direction using multiple 2D multislice acquisitions. Any 2D multislice acquisition can be used for SRR. In this study, the effects of using three different low-resolution acquisition geometries (orthogonal, rotational, and shifted) on SRR images were evaluated and compared to a known standard. Iterative back projection was used for the reconstruction of all three acquisition geometries. The results of the study indicate that super resolution reconstructed images based on orthogonally acquired low-resolution images resulted in reconstructed images with higher SNR and CNR in less acquisition time than those based on rotational and shifted acquisition geometries. However, interpolation artifacts were observed in SRR images based on orthogonal acquisition geometry, particularly when the slice thickness was greater than six times the inplane voxel size. Reconstructions based on rotational geometry appeared smoother than those based on orthogonal geometry, but they required two times longer to acquire than the orthogonal LR images. 1. Introduction MRI is being used more frequently for evaluating morphological phenotypes in genetically engineered mouse models of disease [1]. 3D imaging at the highest spatial resolution is the preferred approach for comparing morphological phenotypes; however, it is not always possible in small animal in vivo imaging settings. This is due to the long acquisition times required to achieve high spatial resolution. Several-factors limit obtaining high-resolution 3D isotropic images in the in vivo settings such as the length of time a mouse can be kept under anesthesia, motion artifacts that are likely to occur during long acquisition protocols that degrade image quality, and increased repetition times required at the high magnetic field strengths used for small animal imaging. Keeping animals under anesthesia for long periods of time (>2？hrs) is not desirable. MRI acquisition protocols with very long repetition times ( ？ms), such as T2-weighted, diffusion-weighted (DW), and inversion recovery imaging are particularly affected by the long scan times required for 3D isotropic imaging. Thus, in vivo MR images in small animal studies are usually acquired using 2D