Deep learning to harmonize MRI scans for better diagnosis and prognosis in multi‐center studies

Abstract

AbstractBackgroundData heterogeneity due to cross‐scanner variations is a major challenge in multi‐center aging and dementia studies. Brain structural measures for the same participant can vary due to scanner differences (manufacturer, scanner age/technology, signal‐to‐noise ratio, pulse sequence design, contrast, resolution) and result in biomarker variability. In this work, we applied basic image processing and deep learning methods (style transfer (ST) and generative adversarial networks (GANs)) for harmonizing T1‐weighted MRI scans across change in vendors (GE to Siemens) and resolution (1x1x1.2mm to 0.8x0.8x0.8mm) and test whether this harmonization improved compatibility of AD biomarker measures.MethodWe utilized training (n=814) and test (n=113 same participants scanned on two scanners close‐in‐time, typically on the same day, with different resolution) data from cognitively impaired and unimpaired participants scanned on GE and Siemens scanners from Mayo Clinic Study of Aging and Mayo ADRC. The harmonization was conducted to translate GE to Siemens. All scans were affine transformed to the same template space, resampled to 1.5 mm3, and bias corrected. Histogram matching was performed using cumulative density functions. A ResNet18 was trained for the ST’s content and style layers. Two types of GANs, conditional GANs (cGAN) and cycle‐consistent GANs (cycleGAN), were constructed. We then measured regional cortical thickness from each image using FreeSurfer‐7.1.1 and compared the thickness measurements from the original and translated scans using intraclass‐correlation (ICC) and Deming regression.ResultIn the test dataset, ST and cycleGAN showed the best performances when comparing the translated GE to Siemens. With ST, the ICC increased (vs. the original scans) slightly for the temporal meta‐ROI (0.956 from 0.954) and more substantially for the frontal pole ROI (0.706 from 0.594). The cycleGAN showed an increase in ICC for the frontal pole ROI (0.610 from 0.594) but not the meta‐ROI (Fig. 1).ConclusionEach method leveraged a different strength. Histogram matching captures contrast, ST extracts textural information, and GANs learn combination of contrast, edge and texture properties. We found that deep learning is a promising approach to cross‐scanner variability. Our comparisons revealed anatomical differences across methods; thus, disease specific measure should be considered for selection of the scanner harmonization method.