Accurate exclusion of kidney regions affected by susceptibility artifact in blood oxygenation level-dependent (BOLD) images using deep-learning-based segmentation

Abstract

Susceptibility artifact (SA) is common in renal blood oxygenation level-dependent (BOLD) images, and including the SA-affected region could induce much error in renal oxygenation quantification. In this paper, we propose to exclude kidney regions affected by SA in gradient echo images with different echo times (TE), based on a deep-learning segmentation approach. For kidney segmentation, a ResUNet was trained with 4000 CT images and then tuned with 60 BOLD images. Verified by a Monte Carlo simulation, the presence of SA leads to a bilinear pattern for the segmented area of kidney as function of TE, and the segmented kidney in the image of turning point’s TE would exclude SA-affected regions. To evaluate the accuracy of excluding SA-affected regions, we compared the SA-free segmentations by the proposed method against manual segmentation by an experienced user for BOLD images of 35 subjects, and found DICE of 93.9% ± 3.4%. For 10 kidneys with severe SA, the DICE was 94.5% ± 1.7%, for 14 with moderate SA, 92.8% ± 4.7%, and for 46 with mild or no SA, 94.3% ± 3.8%. For the three sub-groups of kidneys, correction of SA led to a decrease of R2* of 8.5 ± 2.8, 4.7 ± 1.8, and 1.6 ± 0.9 s−1, respectively. In conclusion, the proposed method is capable of segmenting kidneys in BOLD images and at the same time excluding SA-affected region in a fully automatic way, therefore can potentially improve both speed and accuracy of the quantification procedure of renal BOLD data.