Pratik Mukherjee

Amir Sadikov, Xinlei Pan, Hannah Choi et al.

Diffusion MRI is a non-invasive, in-vivo biomedical imaging method for mapping tissue microstructure. Applications include structural connectivity imaging of the human brain and detecting microstructural neural changes. However, acquiring high signal-to-noise ratio dMRI datasets with high angular and spatial resolution requires prohibitively long scan times, limiting usage in many important clinical settings, especially for children, the elderly, and in acute neurological disorders that may require conscious sedation or general anesthesia. We employ a Swin UNEt Transformers model, trained on augmented Human Connectome Project data and conditioned on registered T1 scans, to perform generalized denoising of dMRI. We also qualitatively demonstrate super-resolution with artificially downsampled HCP data in normal adult volunteers. Remarkably, Swin UNETR can be fine-tuned for an out-of-domain dataset with a single example scan, as we demonstrate on dMRI of children with neurodevelopmental disorders and of adults with acute evolving traumatic brain injury, each cohort scanned on different models of scanners with different imaging protocols at different sites. We exceed current state-of-the-art denoising methods in accuracy and test-retest reliability of rapid diffusion tensor imaging requiring only 90 seconds of scan time. Applied to tissue microstructural modeling of dMRI, Swin UNETR denoising achieves dramatic improvements over the state-of-the-art for test-retest reliability of intracellular volume fraction and free water fraction measurements and can remove heavy-tail noise, improving biophysical modeling fidelity. Swin UNeTR enables rapid diffusion MRI with unprecedented accuracy and reliability, especially for probing biological tissues for scientific and clinical applications. The code and model are publicly available at https://github.com/ucsfncl/dmri-swin.

Qiming Cui, Duygu Tosun, Pratik Mukherjee et al.

Supervised deep learning techniques can be used to generate synthetic 7T MRIs from 3T MRI inputs. This image enhancement process leverages the advantages of ultra-high-field MRI to improve the signal-to-noise and contrast-to-noise ratios of 3T acquisitions. In this paper, we introduce multiple novel 7T synthesization algorithms based on custom-designed variants of the V-Net convolutional neural network. We demonstrate that the V-Net based model has superior performance in enhancing both single-site and multi-site MRI datasets compared to the existing benchmark model. When trained on 3T-7T MRI pairs from 8 subjects with mild Traumatic Brain Injury (TBI), our model achieves state-of-the-art 7T synthesization performance. Compared to previous works, synthetic 7T images generated from our pipeline also display superior enhancement of pathological tissue. Additionally, we implement and test a data augmentation scheme for training models that are robust to variations in the input distribution. This allows synthetic 7T models to accommodate intra-scanner and inter-scanner variability in multisite datasets. On a harmonized dataset consisting of 18 3T-7T MRI pairs from two institutions, including both healthy subjects and those with mild TBI, our model maintains its performance and can generalize to 3T MRI inputs with lower resolution. Our findings demonstrate the promise of V-Net based models for MRI enhancement and offer a preliminary probe into improving the generalizability of synthetic 7T models with data augmentation.

Pratik Mukherjee, Matteo Santilli, Andrea Gasparri et al.

In this paper, we consider two coupled problems for distributed multi-robot systems (MRSs) coordinating with limited field of view (FOV) sensors: adaptive tuning of interaction gains and rejection of sensor attacks. First, a typical shortcoming of distributed control frameworks (e.g., potential fields) is that the overall system behavior is highly sensitive to the gain assigned to relative interactions. Second, MRSs with limited FOV sensors can be more susceptible to sensor attacks aimed at their FOVs, and therefore must be resilient to such attacks. Based on these shortcomings, we propose a comprehensive solution that combines efforts in adaptive gain tuning and attack resilience to the problem of topology control for MRSs with limited FOVs. Specifically, we first derive an adaptive gain tuning scheme based on satisfying nominal pairwise interactions, which yields a dynamic balancing of interaction strengths in a robot's neighborhood. We then model additive sensor and actuator attacks (or faults) and derive H infinity control protocols by employing a static output-feedback technique, guaranteeing bounded L2 gains of the error induced by the attack (fault) signals. Finally, simulation results using ROS Gazebo are provided to support our theoretical findings.

Pratik Mukherjee, Matteo Santilli, Andrea Gasparri et al.

In this paper, we address the problem of stable coordinated motion in multi-robot systems with limited fields of view (FOVs). These problems arise naturally for multi-robot systems that interact based on sensing, such as our case study of multiple unmanned aerial vehicles (UAVs) each equipped with several cameras that are used for detecting neighboring UAVs. In this context, our contributions are: i) first, we derive a framework for studying stable motion and distributed topology control for multi-robot systems with limited FOVs; and ii) Then, we provide experimental results in indoor and challenging outdoor environments (e.g., with wind speeds up to 10 mph) with a team of UAVs to demonstrate the performance of the proposed control framework using a portable multi-robot experimental set-up.

Weicheng Kuo, Christian Häne, Esther Yuh et al.

Deep learning for clinical applications is subject to stringent performance requirements, which raises a need for large labeled datasets. However, the enormous cost of labeling medical data makes this challenging. In this paper, we build a cost-sensitive active learning system for the problem of intracranial hemorrhage detection and segmentation on head computed tomography (CT). We show that our ensemble method compares favorably with the state-of-the-art, while running faster and using less memory. Moreover, our experiments are done using a substantially larger dataset than earlier papers on this topic. Since the labeling time could vary tremendously across examples, we model the labeling time and optimize the return on investment. We validate this idea by core-set selection on our large labeled dataset and by growing it with data from the wild.

Weicheng Kuo, Christian Häne, Esther Yuh et al.

This paper studies the problem of detecting and segmenting acute intracranial hemorrhage on head computed tomography (CT) scans. We propose to solve both tasks as a semantic segmentation problem using a patch-based fully convolutional network (PatchFCN). This formulation allows us to accurately localize hemorrhages while bypassing the complexity of object detection. Our system demonstrates competitive performance with a human expert and the state-of-the-art on classification tasks (0.976, 0.966 AUC of ROC on retrospective and prospective test sets) and on segmentation tasks (0.785 pixel AP, 0.766 Dice score), while using much less data and a simpler system. In addition, we conduct a series of controlled experiments to understand "why" PatchFCN outperforms standard FCN. Our studies show that PatchFCN finds a good trade-off between batch diversity and the amount of context during training. These findings may also apply to other medical segmentation tasks.