Introduction: Voxel-Based Morphometry (VBM) and Source-Based Morphometry (SBM) are two widely used techniques for analyzing structural Magnetic Resonance Imaging (MRI) data of the brain. While VBM is a voxel-wise approach that compares differences in gray and white matter volume, density, or concentration between groups or conditions, SBM identifies patterns of structural variation across the whole brain using independent component analysis (ICA). The purpose of this study is to compare the performance of VBM and SBM in detecting differences in brain structure.Methods: Source-Based-Morphometry through the Fusion Ica Toolbox, and Voxel-Based-Morphometry, with the CAT12 pipeline, were used to test differences and similarities in Parkinson's patients MRI scans and Chronotypes in 33 subjects divided into three groups: a Parkinson's Group (PG), an Early Chronotype Group (EG), and a Late Chronotype Group (LG) (with each group consisting of 11 subjects). Circadian preference, daytime sleepiness and sleep quality were tested, while MRI data were acquired with a 3T scanner.Results: The average age for the EG was 32.1 years old; for the LG it was 30.3 years old; for the PG it was 38.6 years old. SBM statistics showed several clusters surviving the analysis and the conversion to z-map score with a threshold of z > 2. Multiple Regions of Interest (ROI) were identified as different between the groups and the components with the lowest p value (< 0.05) were the 1st one for the PG-EG and the 4th one for the PG-LG analysis. In the Talairach Coordinates analysis, the Middle Frontal Gyrus and the Lentiform Nucleus were identified as denser in GMV or WMV.Conclusion: Our study highlights the importance of choosing the appropriate method for analyzing structural MRI data. While VBM is a powerful technique for identifying local differences in brain structure, SBM provides a more comprehensive view of brain structural variation and can reveal patterns that are not detectable by VBM. Future studies should consider using both VBM and SBM to fully characterize brain structural differences in various clinical and cognitive populations.