This study attempts to highlight the reproducibility problem in clinical diffusion MRI studies by comparing different software in a large diffusion MRI data, collected from multiple sites with 291 schizophrenia patients and 251 healthy controls. We fit diffusion tensor using FSL, MRtrix and Slicer with ordinary-least-squares (OLS) and weighted-least-squares (WLS) methods. To assess biological differences (measured by FA) between controls and patients, we computed effect-sizes (Cohen’s d) at each site using each software. We observed significant software effects with each software package producing significantly different results, when either OLS or WLS, was used.
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