3D CT Radiomic Analysis Improves Detection of Axillary Lymph Node Metastases Compared to Conventional Features in Patients With Locally Advanced Breast Cancer.

OBJECTIVE: Preoperative detection of axillary lymph node metastases (ALNMs) from breast cancer is suboptimal; however, recent work suggests radiomics may improve detection of ALNMs. This study aims to develop a 3D CT radiomics model to improve detection of ALNMs compared to conventional imaging features in patients with locally advanced breast cancer. METHODS: Retrospective chart review was performed on patients referred to a specialty breast cancer center between 2015 and 2020 with US-guided biopsy-proven ALNMs and pretreatment chest CT. One hundred and twelve patients (224 lymph nodes) met inclusion and exclusion criteria and were assigned to discovery (n = 150 nodes) and testing (n = 74 nodes) cohorts. US-biopsy images were referenced in identifying ALNMs on CT, with contralateral nodes taken as negative controls. Positive and negative nodes were assessed for conventional features of lymphadenopathy as well as for 107 radiomic features extracted following 3D segmentation. Diagnostic performance of individual and combined radiomic features was evaluated. RESULTS: The strongest conventional imaging feature of ALNMs was short axis diameter ≥10 mm with a sensitivity of 64%, specificity of 95%, and area under the curve (AUC) of 0.89 (95% CI, 0.84-0.94). Several radiomic features outperformed conventional features, most notably energy, a measure of voxel density magnitude. This feature demonstrated a sensitivity, specificity, and AUC of 91%, 79%, and 0.94 (95% CI, 0.91-0.98) for the discovery cohort. On the testing cohort, energy scored 92%, 81%, and 0.94 (95% CI, 0.89-0.99) for sensitivity, specificity, and AUC, respectively. Combining radiomic features did not improve AUC compared to energy alone (P = .08). CONCLUSION: 3D radiomic analysis represents a promising approach for noninvasive and accurate detection of ALNMs.

Cardiac MRI segmentation with sparse annotations: Ensembling deep learning uncertainty and shape priors.

The performance of deep learning for cardiac magnetic resonance imaging (MRI) segmentation is oftentimes degraded when using small datasets and sparse annotations for training or adapting a pre-trained model to previously unseen datasets. Here, we developed and evaluated an approach to addressing some of these issues to facilitate broader use of deep learning for short-axis cardiac MRI segmentation. We developed a globally optimal label fusion (GOLF) algorithm that enforced spatial smoothness to generate consensus segmentation from segmentation predictions provided by a deep learning ensemble algorithm. The GOLF consensus was entered into an uncertainty-guided coupled continuous kernel cut (ugCCKC) algorithm that employed normalized cut, image-grid continuous regularization, and "nesting" and circular shape priors of the left ventricular myocardium (LVM) and cavity (LVC). In addition, the uncertainty measurements derived from the segmentation predictions were used to constrain the similarity of GOLF and final segmentation. We optimized ugCCKC through upper bound relaxation, for which we developed an efficient coupled continuous max-flow algorithm implemented in an iterative manner. We showed that GOLF yielded average symmetric surface distance (ASSD) 0.2-0.8 mm lower than an averaging method with higher or similar Dice similarity coefficient (DSC). We also demonstrated that ugCCKC incorporating the shape priors improved DSC by 0.01-0.05 and reduced ASSD by 0.1-0.9 mm. In addition, we integrated GOLF and ugCCKC into a deep learning ensemble algorithm by refining the segmentation of an unannotated dataset and using the refined segmentation to update the trained models. With the proposed framework, we demonstrated the capability of using relatively small datasets (5-10 subjects) with sparse (5-25% slices labeled) annotations to train a deep learning algorithm, while achieving DSC of 0.871-0.893 for LVM and 0.933-0.959 for LVC on the LVQuan dataset, and these were 0.844-0.871 for LVM and 0.923-0.931 for LVC on the ACDC dataset. Furthermore, we showed that the proposed approach can be adapted to substantially alleviate the domain shift issue. Moreover, we calculated a number of commonly used LV function measurements using the derived segmentation and observed strong correlations (Pearson r=0.77-1.00, p<0.001) between algorithm and manual LV function analyses. These results suggest that the developed approaches can be used to facilitate broader application of deep learning in research and clinical cardiac MR imaging workflow.

BI-RADS BERT and Using Section Segmentation to Understand Radiology Reports.

Radiology reports are one of the main forms of communication between radiologists and other clinicians, and contain important information for patient care. In order to use this information for research and automated patient care programs, it is necessary to convert the raw text into structured data suitable for analysis. State-of-the-art natural language processing (NLP) domain-specific contextual word embeddings have been shown to achieve impressive accuracy for these tasks in medicine, but have yet to be utilized for section structure segmentation. In this work, we pre-trained a contextual embedding BERT model using breast radiology reports and developed a classifier that incorporated the embedding with auxiliary global textual features in order to perform section segmentation. This model achieved 98% accuracy in segregating free-text reports, sentence by sentence, into sections of information outlined in the Breast Imaging Reporting and Data System (BI-RADS) lexicon, which is a significant improvement over the classic BERT model without auxiliary information. We then evaluated whether using section segmentation improved the downstream extraction of clinically relevant information such as modality/procedure, previous cancer, menopausal status, purpose of exam, breast density, and breast MRI background parenchymal enhancement. Using the BERT model pre-trained on breast radiology reports, combined with section segmentation, resulted in an overall accuracy of 95.9% in the field extraction tasks. This is a 17% improvement, compared to an overall accuracy of 78.9% for field extraction with models using classic BERT embeddings and not using section segmentation. Our work shows the strength of using BERT in the analysis of radiology reports and the advantages of section segmentation by identifying the key features of patient factors recorded in breast radiology reports.

Missed Breast Cancers on MRI in High-Risk Patients: A Retrospective Case-Control Study.

Purpose: To determine if MRI features and molecular subtype influence the detectability of breast cancers on MRI in high-risk patients. Methods and Materials: Breast cancers in a high-risk population of 104 patients were diagnosed following MRI describing a BI-RADS 4-5 lesion. MRI characteristics at the time of diagnosis were compared with previous MRI, where a BI-RADS 1-2-3 lesion was described. Results: There were 77 false-negative MRIs. A total of 51 cancers were overlooked and 26 were misinterpreted. There was no association found between MRI characteristics, the receptor type and the frequency of missed cancers. The main factors for misinterpreted lesions were multiple breast lesions, prior biopsy/surgery and long-term stability. Lesions were mostly overlooked because of their small size and high background parenchymal enhancement. Among missed lesions, 50% of those with plateau kinetics on initial MRI changed for washout kinetics, and 65% of initially progressively enhancing lesions then showed plateau or washout kinetics. There were more basal-like tumours in BRCA1 carriers (50%) than in non-carriers (13%), p = 0.0001, OR = 6.714, 95% CI = [2.058-21.910]. The proportion of missed cancers was lower in BRCA carriers (59%) versus non-carriers (79%), p < 0.05, OR = 2.621, 95% CI = [1.02-6.74]. Conclusions: MRI characteristics or molecular subtype do not influence breast cancer detectability. Lesions in a post-surgical breast should be assessed with caution. Long-term stability does not rule out malignancy and multimodality evaluation is of added value. Lowering the biopsy threshold for lesions with an interval change in kinetics for a type 2 or 3 curve should be considered. There was a higher rate of interval cancers in BRCA 1 patients attributed to lesions more aggressive in nature.

Intensity Augmentation to Improve Generalizability of Breast Segmentation Across Different MRI Scan Protocols.

OBJECTIVE: The segmentation of the breast from the chest wall is an important first step in the analysis of breast magnetic resonance images. 3D U-Nets have been shown to obtain high segmentation accuracy and appear to generalize well when trained on one scanner type and tested on another scanner, provided that a very similar MR protocol is used. There has, however, been little work addressing the problem of domain adaptation when image intensities or patient orientation differ markedly between the training set and an unseen test set. In this work we aim to address this domain shift problem. METHOD: We propose to apply extensive intensity augmentation in addition to geometric augmentation during training. We explored both style transfer and a novel intensity remapping approach as intensity augmentation strategies. For our experiments, we trained a 3D U-Net on T1-weighted scans. We tested our network on T2-weighted scans from the same dataset as well as on an additional independent test set acquired with a T1-weighted TWIST sequence and a different coil configuration. RESULTS: By applying intensity augmentation we increased segmentation performance for the T2-weighted scans from a Dice of 0.71 to 0.88. This performance is very close to the baseline performance of training with T2-weighted scans (0.92). On the T1-weighted dataset we obtained a performance increase from 0.77 to 0.85. CONCLUSION: Our results show that the proposed intensity augmentation increases segmentation performance across different datasets. SIGNIFICANCE: The proposed method can improve whole breast segmentation of clinical MR scans acquired with different protocols.