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.

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.