Japanese quails (Coturnix japonica) divergently selected based on their behavior during a tonic immobility test are an excellent model to study the link between brain morphology and behavior expression. The LTI (Long Tonic Immobility) and STI (Short Tonic Immobility) quail lines differ in their level of emotivity, with LTI quails being selected for their high-trait emotivity. Here, comparing the brain regions of the LTI and STI lines of male Japanese quails, we test the hypothesis that this divergent selection could have influenced brain anatomy, in particular, those regions involved in sensory and emotional processing. The heads of twenty, 10 weeks old male Japanese quails (10 STI and 10 LTI) were imaged ex-vivo using ultra high-resolution (11.7 Tesla) magnetic resonance imaging. The resulting images were used to create a population-averaged quail brain template and manually segmented 3D whole-brain atlas (openly available: https://doi.org/10.5281/zenodo.4700522). The atlas is composed of 191 brain regions, the ventricular system, pineal and pituitary glands. Thanks to this atlas, an exploratory analysis was conducted to compare brain regions between the two lines: the relative volumes of 33 regions were impacted (with 24 larger relative volumes being found in STI). This demonstrates for the first time in male Japanese quail that genetic selection for a specific emotional behavior (tonic immobility) modifies the anatomy of brain regions involved in sensory and emotional processing.