With the feature of noninvasively monitoring the human brain, magnetic resonance imaging (MRI) has become a ubiquitous means to understand how the brain works. Specifically, T1-weighted (T1w) imaging is widely used to examine the brain structure where the cortical thickness, surface area, and brain volumes have been investigated. These T1w-derived phenotypes undergo radical changes during childhood and adolescence, while remaining relatively stable during adulthood. However, stability over a short time (e.g. one year) during adulthood is still unknown. Additionally, how environmental factors such as time-of-day and different daylight lengths could impact the structural brain is also elusive. The main purpose of this study, therefore, was to assess the stability of T1w-derived phenotypes, i.e., cortical thickness, surface area, and brain volumes including subcortical volumes, and to explore the time-of-day and daylight length effects. Accordingly, three subjects in their late 20s, and early 30s and 40s were scanned repeatedly on the same scanner over one year from which a deep brain imaging dataset was constructed with 38, 40, and 25 sessions for subjects 1, 2, and 3, respectively. The T1w-derived phenotypes demonstrated percentage changes within 5% and CVs (coefficients of variance) within 2% for the majority of brain regions. However, several brain regions did show larger variations with percentage changes around 10% and CVs around 5%, such as the temporal pole, the frontal pole, and the entorhinal cortex. More importantly, there were no significant effects of time-of-day and daylight length. Moreover, cortical thickness change was strongly and positively correlated with that of volume while being negatively correlated with that of surface area, illustrating their distinct roles in brain anatomy. Additionally, it was found that apparent head motion causes cortical thickness and volume to be underestimated and surface area to be overestimated. These results indicate that T1w-derived phenotypes are reasonably stable regardless of time-of-day or daylight length, but that head motion should be taken into consideration.SignificanceAssessing the measurement precision and within-subject stability of T1w-derived phenotypes is crucial for accurately estimating brain changes induced by treatments or interventions. Furthermore, understanding within-subject variation enhances our ability to predict behavior and associations with brain phenotypes, which rely heavily on between-subject variation.