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

AbstractThis 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 at Zenodo at https://doi.org/10.5281/zenodo.3555556. 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.HIGHLIGHTS⍰ Open-access high-resolution anatomical MRI template for Fischer 344 rat brain.⍰ Segmented atlas of 71 regions for use as a tool in Fischer 344 preclinical research paradigms.⍰ Analysis of population variability of regional brain volumes.⍰ Analysis of sex-differences in regional brain volumesKEYWORDS: Fischer 344; Structural MRI; Segmentation; Rat brain template; Digital brain atlas; Sex-differences;