A stereotaxic MRI template set for the rat brain with tissue class distribution maps and co-registered anatomical atlas: Application to pharmacological MRI
Introduction
In recent years, functional magnetic resonance imaging (fMRI) methods have been increasingly applied pre-clinically in species such as the rat. This has been driven in part by the potential value of MRI methods in translating findings to and from human studies. Analysis of human fMRI data now routinely involves spatial normalisation to a standard template or reference frame (Friston et al., 1995, Turner et al., 1998, Smith, 2004) and segmentation of the image data into different tissue classes (Ashburner and Friston, 1997, Ashburner and Friston, 2005, Zhang et al., 2001). However, the analysis of functional studies in other species has made relatively selective use of the sophisticated software libraries widely used in human fMRI processing. In the rat, images serving as anatomical underlays or targets for co-registration of data from different subjects have often been study-specific (Lowe et al., 2002, Schwarz et al., 2004, Shah et al., 2004, Kalisch et al., 2004) and arbitrarily oriented. A rat brain MRI template image positioned in the stereotaxic co-ordinates of Paxinos and Watson (1982) has recently been developed (Schweinhardt et al., 2003). However, a further issue in functional image analysis in the rat is that contributions from cerebrospinal fluid (CSF) can confound interpretation of signals from adjacent brain tissue, especially upon spatial smoothing during time series analysis. However, most of the widely used image segmentation algorithms have been designed and validated for human brain images. Tissue class probability maps are available as part of some template sets (Ashburner and Friston, 2005) but are not currently available for the rat.
The assignment of anatomical location to functional effects is critical in the interpretation and analysis of brain imaging studies. In rat brain MRI experiments, this has typically been performed with the aid of standard atlases (for example, Konig and Klippel, 1963, Pelligrino et al., 1979, Paxinos and Watson, 1998, Swanson, 2003) in combination with anatomical features visible within the anatomical MR images. For example, regions of interest are often defined in this way on a common reference image so as to be available to all subjects in the study (Chen et al., 2005, Risterucci et al., 2005, Rausch et al., 2005, Gozzi et al., 2006, Skoubis et al., 2006). The ability to accurately localise the response is of especial issue in pharmacological MRI (phMRI) studies where the functional effect following acute pharmacological challenge often involves a number of disparate brain regions. However, qualitative reference to a separate atlas or selection of atlas figures for image overlays can be limited by misalignment between the MRI and atlas slice planes as well as the fact that MRI functional slices are usually substantially thicker (∼1–2 mm) than the separation of the atlas figures (∼0.1–0.5 mm). The anatomical localisation of functional activation and delineation of regions of interest can thus depend upon a subjective choice of atlas figure as reference and be based on operator-dependent delineation of structure boundaries.
The utility of merging anatomical information from an atlas more closely with functional imaging data has long been recognised. In human studies, co-registration of functional imaging data with anatomical atlas information has been performed since the early 1980s (Bohm et al., 1983, Bohm et al., 1989, Seitz et al., 1990, Greitz et al., 1991), and tools exist to localise effects revealed in fMRI analyses in terms of anatomical regions, either within the same template space (Tzourio-Mazoyer et al., 2002) or via conversion to Tailarach co-ordinates (Lancaster et al., 2000, Maldjian et al., 2003). In the rat, Toga et al. created digital reconstructions of the rat brain based on stereotaxic atlases in the late 1980s, emphasising 3D surface rendering of external and internal structures and the ability to co-visualise functional (at that time predominantly autoradiographic, binding or histological data) and structural information (Toga and Arnicar-Sulze, 1987, Toga et al., 1989, Toga et al., 1995, Toga, 1991). More recently, Leergaard et al. (2003) employed a 3D reconstruction of selected structures from Swanson (1999), affine transformed to MRI data based on manually identified points, to assist interpretation of Mn2+ neural tracing data (Leergaard et al., 2003). Ferris et al. (2005) employed a more complete 3D reconstruction of structures combined from both Paxinos and Watson (1991) and Swanson (1999). In their approach, the brain surface was manually outlined on individual subject MR images and reconstructed as surface shell, before being affine transformed to align with external contours from the atlas.
In this paper we describe a rat brain MRI template set, created from 97 rats, that includes T2-weighted target images for spatial normalisation of MRI studies into stereotaxic space as well as associated tissue class distribution maps to aid segmentation of brain parenchyma from CSF. This facilitates the use of tools available within widely used fMRI software packages (here illustrated with the FSL library; Smith et al., 2004) to automate spatial image processing within the analysis pipeline. A volumetric reconstruction of a standard anatomical atlas (Paxinos and Watson, 1998) is co-localised with the template MRI images and thus available to all data normalised to it. The internal brain structure information enables interactive query of atlas structures as well as unbiased (operator independent) definition of 3D atlas-based volume of interest (VOI) time courses and image masks. As many atlas structures are small relative to the typical resolution of phMRI studies, we also allow for the definition of composite structures as agglomerations of individual atlas structures, providing VOIs on a more appropriate spatial scale. Our explicit motivation was the creation of a tool to aid the analysis of phMRI data in the rat; we demonstrate this with reference to a study of apomorphine, a broad-spectrum dopamine agonist that induces characteristic behaviours in the rat.
Section snippets
Animals
All experiments were carried out in accordance with Italian regulations governing animal welfare and protection. Protocols were also reviewed and consented to by a local animal care committee, in accordance with the guidelines of the Principles of Laboratory Animal Care (NIH publication 86-23, revised 1985).
Acquisition of anatomical images for template set
The MRI template set was created from multi-slice T2-weighted images of the rat brain acquired using a RARE sequence on a Bruker Avance 4.7-T MR scanner with the following acquisition
MRI template and segmentation
The template T2-weighted anatomical image and associated brain parenchyma and CSF distribution maps from the template set are illustrated in Fig. 1. These capture the typical distribution of each within the normal rat brain. The CSF map also includes some small contributions from lipid in the two small dorsal foci visible in the second row from the bottom in Fig. 1(c). These tissue distribution maps, when used as posterior constraints (‘−A’ option), greatly improved the segmentation of brain
Discussion
We have described an MRI template set for the rat brain and shown how it can facilitate the use of standard fMRI spatial normalisation and segmentation algorithms, in an analogous way to common practice in human studies. Such a template set confers several advantages over a study-specific template. The target image for inter-subject co-registration need not be selected or created for each study, and because the template has been aligned with the coordinates of (Paxinos and Watson, 1998),
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