The most popular mouse brain templates are created from ex vivo scans while in vivo templates are not widely available. We have released openly accessible in vivo multi-contrast mouse brain templates and associated tissue probability maps for analyses of in vivo mouse neuroimaging data. Deformation-based morphometry was performed on a test dataset using a study-specific template, our new “MouseIn” template, or the ex vivo DSURQE template. The results using the MouseIn template better matched those using the “gold-standard” study-specific template compared to those using the ex vivo template.
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