An efficient two-step multi-organ registration on abdominal CT via deep-learning based segmentation

Semi-supervised auto-segmentation method for pelvic organ-at-risk in magnetic resonance images based on deep-learning

BACKGROUND AND PURPOSE

In radiotherapy, magnetic resonance (MR) imaging has higher contrast for soft tissues compared to computed tomography (CT) scanning and does not emit radiation. However, manual annotation of the deep learning-based automatic organ-at-risk (OAR) delineation algorithms is expensive, making the collection of large-high-quality annotated datasets a challenge. Therefore, we proposed the low-cost semi-supervised OAR segmentation method using small pelvic MR image annotations.

METHODS

We trained a deep learning-based segmentation model using 116 sets of MR images from 116 patients. The bladder, femoral heads, rectum, and small intestine were selected as OAR regions. To generate the training set, we utilized a semi-supervised method and ensemble learning techniques. Additionally, we employed a post-processing algorithm to correct the self-annotation data. Both 2D and 3D auto-segmentation networks were evaluated for their performance. Furthermore, we evaluated the performance of semi-supervised method for 50 labeled data and only 10 labeled data.

RESULTS

The Dice similarity coefficient (DSC) of the bladder, femoral heads, rectum and small intestine between segmentation results and reference masks is 0.954, 0.984, 0.908, 0.852 only using self-annotation and post-processing methods of 2D segmentation model. The DSC of corresponding OARs is 0.871, 0.975, 0.975, 0.783, 0.724 using 3D segmentation network, 0.896, 0.984, 0.890, 0.828 using 2D segmentation network and common supervised method.

CONCLUSION

The outcomes of our study demonstrate that it is possible to train a multi-OAR segmentation model using small annotation samples and additional unlabeled data. To effectively annotate the dataset, ensemble learning and post-processing methods were employed. Additionally, when dealing with anisotropy and limited sample sizes, the 2D model outperformed the 3D model in terms of performance.

Nested block self-attention multiple resolution residual network for multiorgan segmentation from CT

BACKGROUND

Fast and accurate multiorgans segmentation from computed tomography (CT) scans is essential for radiation treatment planning. Self-attention(SA)-based deep learning methodologies provide higher accuracies than standard methods but require memory and computationally intensive calculations, which restricts their use to relatively shallow networks.

PURPOSE

Our goal was to develop and test a new computationally fast and memory-efficient bidirectional SA method called nested block self-attention (NBSA), which is applicable to shallow and deep multiorgan segmentation networks.

METHODS

A new multiorgan segmentation method combining a deep multiple resolution residual network with computationally efficient SA called nested block SA (MRRN-NBSA) was developed and evaluated to segment 18 different organs from head and neck (HN) and abdomen organs. MRRN-NBSA combines features from multiple image resolutions and feature levels with SA to extract organ-specific contextual features. Computational efficiency is achieved by using memory blocks of fixed spatial extent for SA calculation combined with bidirectional attention flow. Separate models were trained for HN (n = 238) and abdomen (n = 30) and tested on set aside open-source grand challenge data sets for HN (n = 10) using a public domain database of computational anatomy and blinded testing on 20 cases from Beyond the Cranial Vault data set with overall accuracy provided by the grand challenge website for abdominal organs. Robustness to two-rater segmentations was also evaluated for HN cases using the open-source data set. Statistical comparison of MRRN-NBSA against Unet, convolutional network-based SA using criss-cross attention (CCA), dual SA, and transformer-based (UNETR) methods was done by measuring the differences in the average Dice similarity coefficient (DSC) accuracy for all HN organs using the Kruskall-Wallis test, followed by individual method comparisons using paired, two-sided Wilcoxon-signed rank tests at 95% confidence level with Bonferroni correction used for multiple comparisons.

RESULTS

MRRN-NBSA produced an average high DSC of 0.88 for HN and 0.86 for the abdomen that exceeded current methods. MRRN-NBSA was more accurate than the computationally most efficient CCA (average DSC of 0.845 for HN, 0.727 for abdomen). Kruskal-Wallis test showed significant difference between evaluated methods (p=0.00025). Pair-wise comparisons showed significant differences between MRRN-NBSA than Unet (p=0.0003), CCA (p=0.030), dual (p=0.038), and UNETR methods (p=0.012) after Bonferroni correction. MRRN-NBSA produced less variable segmentations for submandibular glands (0.82 ± 0.06) compared to two raters (0.75 ± 0.31).

CONCLUSIONS

MRRN-NBSA produced more accurate multiorgan segmentations than current methods on two different public data sets. Testing on larger institutional cohorts is required to establish feasibility for clinical use.

Salient deformable network for abdominal multiorgan registration

BACKGROUND

Image registration has long been an active research area in the society of medical image computing, which is to perform spatial transformation between a pair of images and establish a point-wise correspondence to achieve spatial consistency.

PURPOSE

Previous work mainly focused on learning complicated deformation fields by maximizing the global-level (i.e., foreground plus background) image similarity. We argue that taking the background similarity into account may not be a good solution, if we only seek the accurate alignment of target organs/regions in real clinical practice.

METHODS

We, therefore, propose a novel concept of S a l i e n t $Salient$ R e g i s t r a t i o n $Registration$ and introduce a novel deformable network equipped with a saliency module. Specifically, a multitask learning-based saliency module is proposed to discriminate the salient regions-of-registration in a semisupervised manner. Then, our deformable network analyzes the intensity and anatomical similarity of salient regions, and finally conducts the salient deformable registration.

RESULTS

We evaluate the efficacy of the proposed network on challenging abdominal multiorgan CT scans. The experimental results demonstrate that the proposed registration network outperforms other state-of-the-art methods, achieving a mean Dice similarity coefficient (DSC) of 40.2%, Hausdorff distance (95 HD) of 20.8 mm, and average symmetric surface distance (ASSD) of 4.58 mm. Moreover, even by training using one labeled data, our network can still attain satisfactory registration performance, with a mean DSC of 39.2%, 95 HD of 21.2 mm, and ASSD of 4.78 mm.

CONCLUSIONS

The proposed network provides an accurate solution for multiorgan registration and has the potential to be used for improving other registration applications. The code is publicly available at https://github.com/Rrrfrr/Salient-Deformable-Network.