An in vivo MRI Template Set for Morphometry, Tissue Segmentation, and fMRI Localization in Rats

Abstract

Over the last decade, several papers have focused on the construction of highly detailed mouse high field magnetic resonance image (MRI) templates via non-linear registration to unbiased reference spaces, allowing for a variety of neuroimaging applications such as robust morphometric analyses. However, work in rats has only provided medium field MRI averages based on linear registration to biased spaces with the sole purpose of approximate functional MRI (fMRI) localization. This precludes any morphometric analysis in spite of the need of exploring in detail the neuroanatomical substrates of diseases in a recent advent of rat models. In this paper we present a new in vivo rat T2 MRI template set, comprising average images of both intensity and shape, obtained via non-linear registration. Also, unlike previous rat template sets, we include white and gray matter probabilistic segmentations, expanding its use to those applications demanding prior-based tissue segmentation, e.g., statistical parametric mapping (SPM) voxel-based morphometry. We also provide a preliminary digitalization of latest Paxinos and Watson atlas for anatomical and functional interpretations within the cerebral cortex. We confirmed that, like with previous templates, forepaw and hindpaw fMRI activations can be correctly localized in the expected atlas structure. To exemplify the use of our new MRI template set, were reported the volumes of brain tissues and cortical structures and probed their relationships with ontogenetic development. Other in vivo applications in the near future can be tensor-, deformation-, or voxel-based morphometry, morphological connectivity, and diffusion tensor-based anatomical connectivity. Our template set, freely available through the SPM extension website, could be an important tool for future longitudinal and/or functional extensive preclinical studies.

Keywords: Paxinos and Watson; SPM; Wistar rats; anatomical connectivity; elastix; fMRI; morphometry; template set.

Figure 1

(A) Individual low resolution MRI of a rat and (B) its intensity histogram. Note that there is a global peak only, though it seems there is an unclear second peak.

Figure 2

Histograms of all intensity corrected MRIs (A) before and (B) after the equalization, showing that the widths and positions of the peaks are transformed to very similar values in each individual.

Figure 3

An axial slice of the (A) average MRI after linear registration to the “average” affine space and the (B) minimal deformation template.

Figure 4

Digitalized Paxinos and Watson atlas, overlaid on the minimal deformation template after being warped to the template space using the approximate thin plate splines (TPS) method, plus further manual corrections.

Figure 5

(A) Filtered low resolution MRI shown in Figure 1 (right) and illustrative picture of the effect of the anisotropic filter on the image in the region enclosed by the yellow box (left): the image is more denoised along the low changes of intensities; the smoothing kernel is a tensor calculated with the gradient of the image at each point. (B) Histogram showing two identifiable peaks corresponding to the white matter and gray matter intensity populations (lilac curve). Four Gaussian distributions were fitted (cyan: non-brain, green: white matter, red: gray matter and blue: cerebrospinal fluid) and three non-parametric curves representing partial volumes. (C) Final tissue segmentations (same color code as the fitted Gaussian curves), after SPM8 post processing of the preliminary segmentations obtained from the histogram analysis.

Figure 6

Axial slices of the gray matter (red), white matter (green), and cerebrospinal fluid (blue) probabilistic segmentations.

Figure 7

Registered orthogonal views of the average MRI template (right) and spatially normalized low resolution MRI (left). In order to provide a comprehensive view, we constructed this picture with the “Check Reg” button of SPM8, which is the usual tool of SPM users for the visualization of registration results.

Figure 8

(A) Tissue segmentations (same color code as 6) and (B) atlasing overlaid on the individual coronal slices of the low resolution MRI in the native space.

Figure 9

The fMRI activations induced by forepaw and hindpaw electrical stimulations. The left (green) and right (violet) forepaw activations are located within the contralateral forelimb regions of the primary somatosensory cortex, denoted as S1FL in the P and W atlas (orange and red regions respectively). Likewise, the left (blue) and right (yellow) activations are within the contralateral hindlimb regions, denoted as S1HL (yellow and cyan regions respectively).