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Neuroimage. 2016 Nov 15;142:656-662. doi: 10.1016/j.neuroimage.2016.03.069. Epub 2016 Apr 1.

Variability of brain anatomy for three common mouse strains.

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Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, Canada. Electronic address:
Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, Canada.
Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.


The way in which brain structures express different morphologies is not fully understood. Here we investigate variability in brain anatomy using ex vivo MRI of three common laboratory mouse strains: in two inbred strains (C57BL/6 and 129S6) and one outbred strain (CD-1). We use Generalised Procrustes Analysis (GPA) to estimate modes of anatomical variability. We find three distinct bilateral modes of anatomical surface variability associated with the motor cortex, the anterior somatosensory, the retrosplenial and the entorhinal cortex. The modes of variability that are associated with the motor cortex and anterior somatosensory cortex are predominantly due to genetic, i.e. strain differences. Next, we specifically test if a particular strain is more variable. We find that only the mode associated with motor cortex size has a slightly larger variance in the outbred CD-1 mice compared to the two inbred strains. This suggests that the hypothesis that outbred strains are more variable in general is not true for brain anatomy and the use of outbred CD-1 mice does probably not come at the price of increased variability. Further, we show that the first two principal components distinguish between the three strains with 91% accuracy. This indicates that neuroanatomical strain differences are captured by considerably fewer dimensions than necessary for atlas-based or voxel-wise testing. Statistical comparisons based on shape models could thus be a powerful complement to traditional atlas and voxel-based methods at detecting gene-related brain differences in mice. Finally, we find that the principal components of individual brain structures are correlated, suggesting a tightly coupled network of interdependent developmental trajectories. These results raise the question to what degree neuroanatomical variability is directly genetically determined or the result of experience and epigenetic mechanisms.


GPA; Genetics; MRI; Mouse strains; Neuroanatomy; PCA; Shape; Surface

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