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Register a new userPSIGAN: Joint probabilistic segmentation and image distribution matching for unpaired cross-modality adaptation based MRI segmentation
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We developed a new joint probabilistic segmentation and image distribution matching generative adversarial network (PSIGAN) for unsupervised domain adaptation (UDA) and multi-organ segmentation from magnetic resonance (MRI) images. Our UDA approach models the co-dependency between images and their segmentation as a joint probability distribution using a new structure discriminator. The structure discriminator computes structure of interest focused adversarial loss by combining the generated pseudo MRI with probabilistic segmentations produced by a simultaneously trained segmentation sub-network. The segmentation sub-network is trained using the pseudo MRI produced by the generator sub-network. This leads to a cyclical optimization of both the generator and segmentation sub-networks that are jointly trained as part of an end-to-end network. Extensive experiments and comparisons against multiple state-of-the-art methods were done on four different MRI sequences totalling 257 scans for generating multi-organ and tumor segmentation. The experiments included, (a) 20 T1-weighted (T1w) in-phase mdixon and (b) 20 T2-weighted (T2w) abdominal MRI for segmenting liver, spleen, left and right kidneys, (c) 162 T2-weighted fat suppressed head and neck MRI (T2wFS) for parotid gland segmentation, and (d) 75 T2w MRI for lung tumor segmentation. Our method achieved an overall average DSC of 0.87 on T1w and 0.90 on T2w for the abdominal organs, 0.82 on T2wFS for the parotid glands, and 0.77 on T2w MRI for lung tumors.
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Deep learning models trained on medical images from a source domain (e.g. imaging modality) often fail when deployed on images from a different target domain, despite imaging common anatomical structures. Deep unsupervised domain adaptation (UDA) aims to improve the performance of a deep neural network model on a target domain, using solely unlabelled target domain data and labelled source domain data. However, current state-of-the-art methods exhibit reduced performance when target data is scarce. In this work, we introduce a new data efficient UDA method for multi-domain medical image segmentation. The proposed method combines a novel VAE-based feature prior matching, which is data-efficient, and domain adversarial training to learn a shared domain-invariant latent space which is exploited during segmentation. Our method is evaluated on a public multi-modality cardiac image segmentation dataset by adapting from the labelled source domain (3D MRI) to the unlabelled target domain (3D CT). We show that by using only one single unlabelled 3D CT scan, the proposed architecture outperforms the state-of-the-art in the same setting. Finally, we perform ablation studies on prior matching and domain adversarial training to shed light on the theoretical grounding of the proposed method.
Unsupervised domain adaptation (UDA) methods have shown their promising performance in the cross-modality medical image segmentation tasks. These typical methods usually utilize a translation network to transform images from the source domain to target domain or train the pixel-level classifier merely using translated source images and original target images. However, when there exists a large domain shift between source and target domains, we argue that this asymmetric structure could not fully eliminate the domain gap. In this paper, we present a novel deep symmetric architecture of UDA for medical image segmentation, which consists of a segmentation sub-network, and two symmetric source and target domain translation sub-networks. To be specific, based on two translation sub-networks, we introduce a bidirectional alignment scheme via a shared encoder and private decoders to simultaneously align features 1) from source to target domain and 2) from target to source domain, which helps effectively mitigate the discrepancy between domains. Furthermore, for the segmentation sub-network, we train a pixel-level classifier using not only original target images and translated source images, but also original source images and translated target images, which helps sufficiently leverage the semantic information from the images with different styles. Extensive experiments demonstrate that our method has remarkable advantages compared to the state-of-the-art methods in both cross-modality Cardiac and BraTS segmentation tasks.
Automatic methods to segment the vestibular schwannoma (VS) tumors and the cochlea from magnetic resonance imaging (MRI) are critical to VS treatment planning. Although supervised methods have achieved satisfactory performance in VS segmentation, they require full annotations by experts, which is laborious and time-consuming. In this work, we aim to tackle the VS and cochlea segmentation problem in an unsupervised domain adaptation setting. Our proposed method leverages both the image-level domain alignment to minimize the domain divergence and semi-supervised training to further boost the performance. Furthermore, we propose to fuse the labels predicted from multiple models via noisy label correction. Our results on the challenge validation leaderboard showed that our unsupervised method has achieved promising VS and cochlea segmentation performance with mean dice score of 0.8261 $pm$ 0.0416; The mean dice value for the tumor is 0.8302 $pm$ 0.0772. This is comparable to the weakly-supervised based method.
Accurate and robust segmentation of lung cancers from CTs is needed to more accurately plan and deliver radiotherapy and to measure treatment response. This is particularly difficult for tumors located close to mediastium, due to low soft-tissue contrast. Therefore, we developed a new cross-modality educed distillation (CMEDL) approach, using unpaired CT and MRI scans, whereby a teacher MRI network guides a student CT network to extract features that signal the difference between foreground and background. Our contribution eliminates two requirements of distillation methods: (i) paired image sets by using an image to image (I2I) translation and (ii) pre-training of the teacher network with a large training set by using concurrent training of all networks. Our framework uses an end-to-end trained unpaired I2I translation, teacher, and student segmentation networks. Our framework can be combined with any I2I and segmentation network. We demonstrate our frameworks feasibility using 3 segmentation and 2 I2I methods. All networks were trained with 377 CT and 82 T2w MRI from different sets of patients. Ablation tests and different strategies for incorporating MRI information into CT were performed. Accuracy was measured using Dice similarity (DSC), surface Dice (sDSC), and Hausdorff distance at the 95$^{th}$ percentile (HD95). The CMEDL approach was significantly (p $<$ 0.001) more accurate than non-CMEDL methods, quantitatively and visually. It produced the highest segmentation accuracy (sDSC of 0.83 $pm$ 0.16 and HD95 of 5.20 $pm$ 6.86mm). CMEDL was also more accurate than using either pMRIs or the combination of CTs with pMRIs for segmentation.
Our contribution is a unified cross-modality feature disentagling approach for multi-domain image translation and multiple organ segmentation. Using CT as the labeled source domain, our approach learns to segment multi-modal (T1-weighted and T2-weighted) MRI having no labeled data. Our approach uses a variational auto-encoder (VAE) to disentangle the image content from style. The VAE constrains the style feature encoding to match a universal prior (Gaussian) that is assumed to span the styles of all the source and target modalities. The extracted image style is converted into a latent style scaling code, which modulates the generator to produce multi-modality images according to the target domain code from the image content features. Finally, we introduce a joint distribution matching discriminator that combines the translated images with task-relevant segmentation probability maps to further constrain and regularize image-to-image (I2I) translations. We performed extensive comparisons to multiple state-of-the-art I2I translation and segmentation methods. Our approach resulted in the lowest average multi-domain image reconstruction error of 1.34$pm$0.04. Our approach produced an average Dice similarity coefficient (DSC) of 0.85 for T1w and 0.90 for T2w MRI for multi-organ segmentation, which was highly comparable to a fully supervised MRI multi-organ segmentation network (DSC of 0.86 for T1w and 0.90 for T2w MRI).
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