Field-of-view extension for brain diffusion MRI via deep generative models

Abstract

Purpose: In brain diffusion magnetic resonance imaging (dMRI), the volumetric and bundle analyses of whole-brain tissue microstructure and connectivity can be severely impeded by an incomplete field of view (FOV). We aim to develop a method for imputing the missing slices directly from existing dMRI scans with an incomplete FOV. We hypothesize that the imputed image with a complete FOV can improve whole-brain tractography for corrupted data with an incomplete FOV. Therefore, our approach provides a desirable alternative to discarding the valuable brain dMRI data, enabling subsequent tractography analyses that would otherwise be challenging or unattainable with corrupted data.

Approach: We propose a framework based on a deep generative model that estimates the absent brain regions in dMRI scans with an incomplete FOV. The model is capable of learning both the diffusion characteristics in diffusion-weighted images (DWIs) and the anatomical features evident in the corresponding structural images for efficiently imputing missing slices of DWIs in the incomplete part of the FOV.

Results: For evaluating the imputed slices, on the Wisconsin Registry for Alzheimer's Prevention (WRAP) dataset, the proposed framework achieved ${\mathrm{PSNR}}_{b0}=22.397$ , ${\mathrm{SSIM}}_{b0}=0.905$ , ${\mathrm{PSNR}}_{b1300}=22.479$ , and ${\mathrm{SSIM}}_{b1300}=0.893$ ; on the National Alzheimer's Coordinating Center (NACC) dataset, it achieved ${\mathrm{PSNR}}_{b0}=21.304$ , ${\mathrm{SSIM}}_{b0}=0.892$ , ${\mathrm{PSNR}}_{b1300}=21.599$ , and ${\mathrm{SSIM}}_{b1300}=0.877$ . The proposed framework improved the tractography accuracy, as demonstrated by an increased average Dice score for 72 tracts ( $p<0.001$ ) on both the WRAP and NACC datasets.

Conclusions: Results suggest that the proposed framework achieved sufficient imputation performance in brain dMRI data with an incomplete FOV for improving whole-brain tractography, thereby repairing the corrupted data. Our approach achieved more accurate whole-brain tractography results with an extended and complete FOV and reduced the uncertainty when analyzing bundles associated with Alzheimer's disease.

Keywords: diffusion MRI; generative model; imputation; medical image synthesis.