Soorena Salari

Amirhossein Rasoulian, Soorena Salari, Yiming Xiao

Intracranial hemorrhage (ICH) is a life-threatening medical emergency that requires timely and accurate diagnosis for effective treatment and improved patient survival rates. While deep learning techniques have emerged as the leading approach for medical image analysis and processing, the most commonly employed supervised learning often requires large, high-quality annotated datasets that can be costly to obtain, particularly for pixel/voxel-wise image segmentation. To address this challenge and facilitate ICH treatment decisions, we introduce a novel weakly supervised method for ICH segmentation, utilizing a Swin transformer trained on an ICH classification task with categorical labels. Our approach leverages a hierarchical combination of head-wise gradient-infused self-attention maps to generate accurate image segmentation. Additionally, we conducted an exploratory study on different learning strategies and showed that binary ICH classification has a more positive impact on self-attention maps compared to full ICH subtyping. With a mean Dice score of 0.44, our technique achieved similar ICH segmentation performance as the popular U-Net and Swin-UNETR models with full supervision and outperformed a similar weakly supervised approach using GradCAM, demonstrating the excellent potential of the proposed framework in challenging medical image segmentation tasks. Our code is available at https://github.com/HealthX-Lab/HGI-SAM.

Soorena Salari, Amirhossein Rasoulian, Hassan Rivaz et al.

Homologous anatomical landmarks between medical scans are instrumental in quantitative assessment of image registration quality in various clinical applications, such as MRI-ultrasound registration for tissue shift correction in ultrasound-guided brain tumor resection. While manually identified landmark pairs between MRI and ultrasound (US) have greatly facilitated the validation of different registration algorithms for the task, the procedure requires significant expertise, labor, and time, and can be prone to inter- and intra-rater inconsistency. So far, many traditional and machine learning approaches have been presented for anatomical landmark detection, but they primarily focus on mono-modal applications. Unfortunately, despite the clinical needs, inter-modal/contrast landmark detection has very rarely been attempted. Therefore, we propose a novel contrastive learning framework to detect corresponding landmarks between MRI and intra-operative US scans in neurosurgery. Specifically, two convolutional neural networks were trained jointly to encode image features in MRI and US scans to help match the US image patch that contain the corresponding landmarks in the MRI. We developed and validated the technique using the public RESECT database. With a mean landmark detection accuracy of 5.88+-4.79 mm against 18.78+-4.77 mm with SIFT features, the proposed method offers promising results for MRI-US landmark detection in neurosurgical applications for the first time.

Soorena Salari, Amirhossein Rasoulian, Hassan Rivaz et al.

In brain tumor resection, accurate removal of cancerous tissues while preserving eloquent regions is crucial to the safety and outcomes of the treatment. However, intra-operative tissue deformation (called brain shift) can move the surgical target and render the pre-surgical plan invalid. Intra-operative ultrasound (iUS) has been adopted to provide real-time images to track brain shift, and inter-modal (i.e., MRI-iUS) registration is often required to update the pre-surgical plan. Quality control for the registration results during surgery is important to avoid adverse outcomes, but manual verification faces great challenges due to difficult 3D visualization and the low contrast of iUS. Automatic algorithms are urgently needed to address this issue, but the problem was rarely attempted. Therefore, we propose a novel deep learning technique based on 3D focal modulation in conjunction with uncertainty estimation to accurately assess MRI-iUS registration errors for brain tumor surgery. Developed and validated with the public RESECT clinical database, the resulting algorithm can achieve an estimation error of 0.59+-0.57 mm.

Soorena Salari, Amirhossein Rasoulian, Hassan Rivaz et al.

Early surgical treatment of brain tumors is crucial in reducing patient mortality rates. However, brain tissue deformation (called brain shift) occurs during the surgery, rendering pre-operative images invalid. As a cost-effective and portable tool, intra-operative ultrasound (iUS) can track brain shift, and accurate MRI-iUS registration techniques can update pre-surgical plans and facilitate the interpretation of iUS. This can boost surgical safety and outcomes by maximizing tumor removal while avoiding eloquent regions. However, manual assessment of MRI-iUS registration results in real-time is difficult and prone to errors due to the 3D nature of the data. Automatic algorithms that can quantify the quality of inter-modal medical image registration outcomes can be highly beneficial. Therefore, we propose a novel deep-learning (DL) based framework with the Swin UNETR to automatically assess 3D-patch-wise dense error maps for MRI-iUS registration in iUS-guided brain tumor resection and show its performance with real clinical data for the first time.

Amirhossein Rasoulian, Arash Harirpoush, Soorena Salari et al.

Accurate identification and quantification of unruptured intracranial aneurysms (UIAs) is crucial for the risk assessment and treatment of this cerebrovascular disorder. Current 2D manual assessment on 3D magnetic resonance angiography (MRA) is suboptimal and time-consuming. In addition, one major issue in medical image segmentation is the need for large well-annotated data, which can be expensive to obtain. Techniques that mitigate this requirement, such as weakly supervised learning with coarse labels are highly desirable. In the paper, we propose FocalSegNet, a novel 3D focal modulation UNet, to detect an aneurysm and offer an initial, coarse segmentation of it from time-of-flight MRA image patches, which is further refined with a dense conditional random field (CRF) post-processing layer to produce a final segmentation map. We trained and evaluated our model on a public dataset, and in terms of UIA detection, our model showed a low false-positive rate of 0.21 and a high sensitivity of 0.80. For voxel-wise aneurysm segmentation, we achieved a Dice score of 0.68 and a 95% Hausdorff distance of ~0.95 mm, demonstrating its strong performance. We evaluated our algorithms against the state-of-the-art 3D Residual-UNet and Swin-UNETR, and illustrated the superior performance of our proposed FocalSegNet, highlighting the advantages of employing focal modulation for this task.

Soorena Salari, Arash Harirpoush, Hassan Rivaz et al.

Anatomical landmark detection in medical images is essential for various clinical and research applications, including disease diagnosis and surgical planning. However, manual landmark annotation is time-consuming and requires significant expertise. Existing deep learning (DL) methods often require large amounts of well-annotated data, which are costly to acquire. In this paper, we introduce CABLD, a novel self-supervised DL framework for 3D brain landmark detection in unlabeled scans with varying contrasts by using only a single reference example. To achieve this, we employed an inter-subject landmark consistency loss with an image registration loss while introducing a 3D convolution-based contrast augmentation strategy to promote model generalization to new contrasts. Additionally, we utilize an adaptive mixed loss function to schedule the contributions of different sub-tasks for optimal outcomes. We demonstrate the proposed method with the intricate task of MRI-based 3D brain landmark detection. With comprehensive experiments on four diverse clinical and public datasets, including both T1w and T2w MRI scans at different MRI field strengths, we demonstrate that CABLD outperforms the state-of-the-art methods in terms of mean radial errors (MREs) and success detection rates (SDRs). Our framework provides a robust and accurate solution for anatomical landmark detection, reducing the need for extensively annotated datasets and generalizing well across different imaging contrasts. Our code is publicly available at https://github.com/HealthX-Lab/CABLD.

Moloud Abdar, Soorena Salari, Sina Qahremani et al.

The COVID-19 (Coronavirus disease 2019) pandemic has become a major global threat to human health and well-being. Thus, the development of computer-aided detection (CAD) systems that are capable to accurately distinguish COVID-19 from other diseases using chest computed tomography (CT) and X-ray data is of immediate priority. Such automatic systems are usually based on traditional machine learning or deep learning methods. Differently from most of existing studies, which used either CT scan or X-ray images in COVID-19-case classification, we present a simple but efficient deep learning feature fusion model, called UncertaintyFuseNet, which is able to classify accurately large datasets of both of these types of images. We argue that the uncertainty of the model's predictions should be taken into account in the learning process, even though most of existing studies have overlooked it. We quantify the prediction uncertainty in our feature fusion model using effective Ensemble MC Dropout (EMCD) technique. A comprehensive simulation study has been conducted to compare the results of our new model to the existing approaches, evaluating the performance of competing models in terms of Precision, Recall, F-Measure, Accuracy and ROC curves. The obtained results prove the efficiency of our model which provided the prediction accuracy of 99.08\% and 96.35\% for the considered CT scan and X-ray datasets, respectively. Moreover, our UncertaintyFuseNet model was generally robust to noise and performed well with previously unseen data. The source code of our implementation is freely available at: https://github.com/moloud1987/UncertaintyFuseNet-for-COVID-19-Classification.

Soorena Salari, Hassan Rivaz, Yiming Xiao

Automated detection of anatomical landmarks plays a crucial role in many diagnostic and surgical applications. Progresses in deep learning (DL) methods have resulted in significant performance enhancement in tasks related to anatomical landmark detection. While current research focuses on accurately localizing these landmarks in medical scans, the importance of inter-rater annotation variability in building DL models is often overlooked. Understanding how inter-rater variability impacts the performance and reliability of the resulting DL algorithms, which are crucial for clinical deployment, can inform the improvement of training data construction and boost DL models' outcomes. In this paper, we conducted a thorough study of different annotation-fusion strategies to preserve inter-rater variability in DL models for anatomical landmark detection, aiming to boost the performance and reliability of the resulting algorithms. Additionally, we explored the characteristics and reliability of four metrics, including a novel Weighted Coordinate Variance metric to quantify landmark detection uncertainty/inter-rater variability. Our research highlights the crucial connection between inter-rater variability, DL-models performances, and uncertainty, revealing how different approaches for multi-rater landmark annotation fusion can influence these factors.

Soorena Salari, Catherine Spino, Laurie-Anne Pharand et al.

Accurate tissue motion tracking is critical to ensure treatment outcome and safety in 2D-Cine MRI-guided radiotherapy. This is typically achieved by registration of sequential images, but existing methods often face challenges with large misalignments and lack of interpretability. In this paper, we introduce DINOMotion, a novel deep learning framework based on DINOv2 with Low-Rank Adaptation (LoRA) layers for robust, efficient, and interpretable motion tracking. DINOMotion automatically detects corresponding landmarks to derive optimal image registration, enhancing interpretability by providing explicit visual correspondences between sequential images. The integration of LoRA layers reduces trainable parameters, improving training efficiency, while DINOv2's powerful feature representations offer robustness against large misalignments. Unlike iterative optimization-based methods, DINOMotion directly computes image registration at test time. Our experiments on volunteer and patient datasets demonstrate its effectiveness in estimating both linear and nonlinear transformations, achieving Dice scores of 92.07% for the kidney, 90.90% for the liver, and 95.23% for the lung, with corresponding Hausdorff distances of 5.47 mm, 8.31 mm, and 6.72 mm, respectively. DINOMotion processes each scan in approximately 30ms and consistently outperforms state-of-the-art methods, particularly in handling large misalignments. These results highlight its potential as a robust and interpretable solution for real-time motion tracking in 2D-Cine MRI-guided radiotherapy.

Soorena Salari, Nasser Sadati

This paper presents a novel feature fusion-based deep learning model (called CASU2Net) for fault detection in offshore wind turbines. The proposed CASU2Net model benefits of a two-step early fusion to enrich features in the final stage. Moreover, since previous studies did not consider uncertainty while model developing and also predictions, we take advantage of Monte Carlo dropout (MC dropout) to enhance the certainty of the results. To design fault detection model, we use five sensors and a sliding window to exploit the inherent temporal information contained in the raw time-series data obtained from sensors. The proposed model uses the nonlinear relationships among multiple sensor variables and the temporal dependency of each sensor on others which considerably increases the performance of fault detection model. A 10-fold cross-validation approach is used to verify the generalization of the model and evaluate the classification metrics. To evaluate the performance of the model, simulated data from a benchmark floating offshore wind turbine (FOWT) with supervisory control and data acquisition (SCADA) are used. The results illustrate that the proposed model would accurately disclose and classify more than 99% of the faults. Moreover, it is generalizable and can be used to detect faults for different types of systems.