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We present a novel multivariate approach called source based morphometry (SBM) to study the novel structural MRI phase images and get sources of relative gray matter and white matter differences between patients and healthy controls. SBM considers the information cross brain voxels and provides spatially maximal independent sources about localization of changes. The structural MRI phase images efficiently summarize the relationship that exists between the gray and white matter without having to increase the dimensionality of the problem. SBM was then applied to the phase images. Results identified patient versus control differences in gray matter and white matter for visual-motor cortex as well as other areas. These interesting findings show that SBM is a useful multivariate approach for studying the brain. Moreover, the use of structural MRI phase images to joint gray and white matter together provides a significant advantage.