An MRI-Derived Neuroanatomical Atlas of the Fischer 344 Rat Brain - PubMed (original) (raw)

An MRI-Derived Neuroanatomical Atlas of the Fischer 344 Rat Brain

Dana Goerzen et al. Sci Rep. 2020.

Abstract

This paper reports the development of a high-resolution 3-D MRI atlas of the Fischer 344 adult rat brain. The atlas is a 60 μm isotropic image volume composed of 256 coronal slices with 71 manually delineated structures and substructures. The atlas was developed using Pydpiper image registration pipeline to create an average brain image of 41 four-month-old male and female Fischer 344 rats. Slices in the average brain image were then manually segmented, individually and bilaterally, on the basis of image contrast in conjunction with Paxinos and Watson's (2007) stereotaxic rat brain atlas. Summary statistics (mean and standard deviation of regional volumes) are reported for each brain region across the sample used to generate the atlas, and a statistical comparison of a chosen subset of regional brain volumes between male and female rats is presented. On average, the coefficient of variation of regional brain volumes across all rats in our sample was 4%, with no individual brain region having a coefficient of variation greater than 13%. A full description of methods used, as well as the atlas, the template that the atlas was derived from, and a masking file, can be found on Zenodo at www.zenodo.org/record/3700210\. To our knowledge, this is the first MRI atlas created using Fischer 344 rats and will thus provide an appropriate neuroanatomical model for researchers working with this strain.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1

Figure 1

Flow chart demonstrating the iterative process used to produce the template image used for segmentation, as described in Section 2.3.

Figure 2

Figure 2

Left column: the averaged brain, which served as a template for structural delineation. Red crosshairs on transverse and sagittal view (middle and bottom) indicate the positions of the other planes. Right column: the atlas file is overlaid onto the template file. Delineation and refinement were primarily performed using the coronal sections, though further refinement was done in both the sagittal and axial planes. Top row: annotated over the left hemisphere of both coronal images are the structural regions that the label tags represent. Middle and Bottom row show transverse and sagittal views respectively; CC, corpus callosum and external capsule; cg, cingulum; cor, cortex; cp, cerebral peduncles; DG, dentate gyrus; eml, external medullary lamina; f, fornix; fr, fasciculus retroflexus; hyp, hypothalamus; hpc, hippocampal CA subfields; LV, lateral ventricle; ml, medial lemniscus; MM, mammillary bodies; opt, optic tract; PAG, periaqueductal gray; 3 V, third ventricle.

Figure 3

Figure 3

In the left column is the template brain, and in the right column is the template brain with the atlas file superimposed. This figure shows a series of coronal slices at different regions of the cortex. The positions of representative slices are marked with dashed lines in a mid-sagittal slice with labels A–D.

Figure 4

Figure 4

On the left is the template brain, and on the right is the template brain with the atlas file superimposed. Clear boundaries are identifiable between all of the major lobes. White matter and Arbor Vitae were indistinguishable from each other based on the resolution of the image. All the hindbrain nuclei were delineated as one structure due to poor resolution and low contrast levels in the hindbrain.

Figure 5

Figure 5

Comparison of the coefficient of variation (CV) for selected structures across all 41 subjects. The volume of most of the 71 structures varies between 4% and 8% across subjects. As expected, the ventricular system displays increased variation across subjects (Fourth Ventricle: 12.2%).

References

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