High-resolution 3D MRI of mouse brain reveals small cerebral structures in vivo

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Abstract

This work demonstrates technical approaches to high-quality magnetic resonance imaging (MRI) of small structures of the mouse brain in vivo. It turns out that excellent soft-tissue contrast requires the reduction of partial volume effects by using 3D MRI at high (isotropic) resolution with linear voxel dimensions of about 100–150 μm. The long T2* relaxation times at relatively low magnetic fields (2.35 T) offer the benefit of a small receiver bandwidth (increased signal-to-noise) at a moderate echo time which together with the small voxel size avoids visual susceptibility artifacts. For measuring times of 1–1.5 h both T1-weighted (FLASH) and T2-weighted (Fast Spin-Echo) 3D MRI acquisitions exhibit detailed anatomical insights in accordance with histological sections from a mouse brain atlas. Preliminary applications address the identification of neuroanatomical variations in different mouse strains and the use of Mn2+ as a T1 contrast agent for neuroaxonal tracing of fiber tracts within the mouse visual pathway.

Introduction

During the past decade progress in neurogenetics has considerably facilitated the development of mutant mice. Since noninvasive magnetic resonance techniques provide structural, metabolic, and functional insights into the central nervous system in vivo and, furthermore, allow for repeated studies of the same animal, magnetic resonance imaging (MRI) and magnetic resonance spectroscopy are expected to become important research tools in system-oriented neurobiology with foreseeable contributions to functional genomics and considerable potential to bridge the gap to clinical applications.

Previous MRI studies of the brain of normal and/or mutant mice may be divided into two categories (for reviews, see Budinger et al., 1999, Jacobs et al., 1999b, Benveniste et al., 2000, Jacobs and Cherry, 2001, Kooy et al., 2001). First of all, post mortem imaging of excised specimen has reached near-microscopic spatial resolution as good as 15×15×15 μm3 and is commonly performed at magnetic field strengths of 9.4 T or higher (Kornguth et al., 1994, Smith et al., 1994, Jacobs et al., 1999a). Although such studies yield geometrically undistorted three-dimensional representations of the brain or selected structures and thus extend histological reconstructions, they sacrifice the inherent noninvasiveness of MRI and, for example, exclude follow-up measurements during disease progression and for the evaluation of novel therapeutic interventions.

In contrast, the few in vivo MRI studies of mouse brain reported so far cover a wide range of voxel sizes and field strengths, for example 98×156×1500 μm3 at 11.7 T (Dubowitz et al., 2000), 140×140×1200 μm3 at 4.7 T (Hesselbarth et al., 1998), 156×156×1000 μm3 at 14 T (Yang et al., 1999), 100×200×900 μm3 at 2.39 T (Munasinghe et al., 1995), 78×156×343 μm3 at 7 T (Kooy et al., 1999), and 150×150×150 μm3 at 4.7 T (Xu et al., 1998). It is of interest to note, that most approaches emphasize a high in-plane resolution at the expense of a much poorer section thickness. While acceptable for larger animals and humans, the disregard of high spatial resolution in all three dimensions compromises the delineation of small structures (e.g., hippocampal formation) in the mouse brain (typical length 14 mm, width 9 mm, height 6 mm) by significant partial volume effects.

The purpose of this study was (i) to develop T1- and T2-weighted 3D MRI protocols for high-resolution studies of mouse brain in vivo which allow for the identification of small cerebral structures, (ii) to perform a direct comparison of anatomical structures with histological sections of C57BL/6J mice as the most frequently used strain in gene knockout studies, and (iii) to examine the potential of these protocols for phenotyping of different mouse strains and in vivo tracing of axonal fiber connections after Mn2+ administration. A preliminary account has been given in abstract form (Natt et al., 2002).

Section snippets

Materials and methods

All studies were performed in accordance with German animal protection laws and approved by the responsible governmental authority. Young adult NMRI mice (n=18, female), C57BL/6J mice (n=4, male), and BALB/c mice (n=4, male) underwent MRI examinations at 2.35 T using a MRBR 4.7/400 mm magnet (Magnex Scientific, Abingdon, England) equipped with BGA20 gradients (100 mT m−1) driven by a DBX system (Bruker Biospin, Ettlingen, Germany).

For in vivo studies the animals were intubated and kept under

Partial volume effects and beyond

The most enlightening aspect of the use of 3D MRI at suitable anatomical resolution is the unraveling of structural detail by removing partial volume effects. Fig. 2 demonstrates how unreasonably low resolution obscures contrast by merging signal intensity differences from neighboring though distinct structures. For image acquisitions with section thicknesses of 500 μm or more (left two columns of Fig. 2), most of the tissue contrast is lost. While coarse structures of the mouse brain (e.g.

Conclusion

It has been shown that high-resolution 3D MRI studies of mouse brain in vivo yield excellent SNR and soft-tissue contrast. In this context, the use of isotropic or near-isotropic spatial resolution with linear voxel dimensions of about 100–150 μm (corresponding to volumes of 1.0–3.4 nl) turns out to be a prerequisite for minimizing partial volume effects and thus enhancing the contrast of the small anatomical structures of mouse brain. The surprisingly good performance of the low field, in

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