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A new smart-cropping pipeline for prostate segmentation using deep learning networks
Jul 07, 2021
Prostate segmentation from magnetic resonance imaging (MRI) is a challenging task. In recent years, several network architectures have been proposed to automate this process and alleviate the burden of manual annotation. Although the performance of these models has achieved promising results, there is still room for improvement before these models can be used safely and effectively in clinical practice. One of the major challenges in prostate MR image segmentation is the presence of class imbalance in the image labels where the background pixels dominate over the prostate. In the present work we propose a DL-based pipeline for cropping the region around the prostate from MRI images to produce a more balanced distribution of the foreground pixels (prostate) and the background pixels and improve segmentation accuracy. The effect of DL-cropping for improving the segmentation performance compared to standard center-cropping is assessed using five popular DL networks for prostate segmentation, namely U-net, U-net+, Res Unet++, Bridge U-net and Dense U-net. The proposed smart-cropping outperformed the standard center cropping in terms of segmentation accuracy for all the evaluated prostate segmentation networks. In terms of Dice score, the highest improvement was achieved for the U-net+ and ResU-net++ architectures corresponding to 8.9% and 8%, respectively.
A multicenter study on radiomic features from T$_2$-weighted images of a customized MR pelvic phantom setting the basis for robust radiomic models in clinics
May 18, 2020
In this study we investigated the repeatability and reproducibility of radiomic features extracted from MRI images and provide a workflow to identify robust features. 2D and 3D T$_2$-weighted images of a pelvic phantom were acquired on three scanners of two manufacturers and two magnetic field strengths. The repeatability and reproducibility of the radiomic features were assessed respectively by intraclass correlation coefficient (ICC) and concordance correlation coefficient (CCC), considering repeated acquisitions with or without phantom repositioning, and with different scanner/acquisition type, and acquisition parameters. The features showing ICC/CCC > 0.9 were selected, and their dependence on shape information (Spearman's $\rho$> 0.8) was analyzed. They were classified for their ability to distinguish textures, after shuffling voxel intensities. From 944 2D features, 79.9% to 96.4% showed excellent repeatability in fixed position across all scanners. Much lower range (11.2% to 85.4%) was obtained after phantom repositioning. 3D extraction did not improve repeatability performance. Excellent reproducibility between scanners was observed in 4.6% to 15.6% of the features, at fixed imaging parameters. 82.4% to 94.9% of features showed excellent agreement when extracted from images acquired with TEs 5 ms apart (values decreased when increasing TE intervals) and 90.7% of the features exhibited excellent reproducibility for changes in TR. 2.0% of non-shape features were identified as providing only shape information. This study demonstrates that radiomic features are affected by specific MRI protocols. The use of our radiomic pelvic phantom allowed to identify unreliable features for radiomic analysis on T$_2$-weighted images. This paper proposes a general workflow to identify repeatable, reproducible, and informative radiomic features, fundamental to ensure robustness of clinical studies.