Jisoo Lee

Joomee Song, Juyoung Hahm, Jisoo Lee et al.

Automated segmentation and volumetry of brain magnetic resonance imaging (MRI) scans are essential for the diagnosis of Parkinson's disease (PD) and Parkinson's plus syndromes (P-plus). To enhance the diagnostic performance, we adopt deep learning (DL) models in brain segmentation and compared their performance with the gold-standard non-DL method. We collected brain MRI scans of healthy controls (n=105) and patients with PD (n=105), multiple systemic atrophy (n=132), and progressive supranuclear palsy (n=69) at Samsung Medical Center from January 2017 to December 2020. Using the gold-standard non-DL model, FreeSurfer (FS), we segmented six brain structures: midbrain, pons, caudate, putamen, pallidum, and third ventricle, and considered them as annotating data for DL models, the representative V-Net and UNETR. The Dice scores and area under the curve (AUC) for differentiating normal, PD, and P-plus cases were calculated. The segmentation times of V-Net and UNETR for the six brain structures per patient were 3.48 +- 0.17 and 48.14 +- 0.97 s, respectively, being at least 300 times faster than FS (15,735 +- 1.07 s). Dice scores of both DL models were sufficiently high (>0.85), and their AUCs for disease classification were superior to that of FS. For classification of normal vs. P-plus and PD vs. multiple systemic atrophy (cerebellar type), the DL models and FS showed AUCs above 0.8. DL significantly reduces the analysis time without compromising the performance of brain segmentation and differential diagnosis. Our findings may contribute to the adoption of DL brain MRI segmentation in clinical settings and advance brain research.

Hanxue Gu, Roy Colglazier, Haoyu Dong et al.

Magnetic Resonance Imaging (MRI) is pivotal in radiology, offering non-invasive and high-quality insights into the human body. Precise segmentation of MRIs into different organs and tissues would be highly beneficial since it would allow for a higher level of understanding of the image content and enable important measurements, which are essential for accurate diagnosis and effective treatment planning. Specifically, segmenting bones in MRI would allow for more quantitative assessments of musculoskeletal conditions, while such assessments are largely absent in current radiological practice. The difficulty of bone MRI segmentation is illustrated by the fact that limited algorithms are publicly available for use, and those contained in the literature typically address a specific anatomic area. In our study, we propose a versatile, publicly available deep-learning model for bone segmentation in MRI across multiple standard MRI locations. The proposed model can operate in two modes: fully automated segmentation and prompt-based segmentation. Our contributions include (1) collecting and annotating a new MRI dataset across various MRI protocols, encompassing over 300 annotated volumes and 8485 annotated slices across diverse anatomic regions; (2) investigating several standard network architectures and strategies for automated segmentation; (3) introducing SegmentAnyBone, an innovative foundational model-based approach that extends Segment Anything Model (SAM); (4) comparative analysis of our algorithm and previous approaches; and (5) generalization analysis of our algorithm across different anatomical locations and MRI sequences, as well as an external dataset. We publicly release our model at https://github.com/mazurowski-lab/SegmentAnyBone.

Yuwen Chen, Nicholas Konz, Hanxue Gu et al.

Preserving object structure through image-to-image translation is crucial, particularly in applications such as medical imaging (e.g., CT-to-MRI translation), where downstream clinical and machine learning applications will often rely on such preservation. However, typical image-to-image translation algorithms prioritize perceptual quality with respect to output domain features over the preservation of anatomical structures. To address these challenges, we first introduce a novel metric to quantify the structural bias between domains which must be considered for proper translation. We then propose ContourDiff, a novel image-to-image translation algorithm that leverages domain-invariant anatomical contour representations of images to preserve the anatomical structures during translation. These contour representations are simple to extract from images, yet form precise spatial constraints on their anatomical content. ContourDiff applies an input image contour representation as a constraint at every sampling step of a diffusion model trained in the output domain, ensuring anatomical content preservation for the output image. We evaluate our method on challenging lumbar spine and hip-and-thigh CT-to-MRI translation tasks, via (1) the performance of segmentation models trained on translated images applied to real MRIs, and (2) the foreground FID and KID of translated images with respect to real MRIs. Our method outperforms other unpaired image translation methods by a significant margin across almost all metrics and scenarios. Moreover, it achieves this without the need to access any input domain information during training.

Eun Som Jeon, Sinjini Mitra, Jisoo Lee et al.

Human gait analysis with wearable sensors has been widely used in various applications, such as daily life healthcare, rehabilitation, physical therapy, and clinical diagnostics and monitoring. In particular, ground reaction force (GRF) provides critical information about how the body interacts with the ground during locomotion. Although instrumented treadmills have been widely used as the gold standard for measuring GRF during walking, their lack of portability and high cost make them impractical for many applications. As an alternative, low-cost, portable, wearable insole sensors have been utilized to measure GRF; however, these sensors are susceptible to noise and disturbance and are less accurate than treadmill measurements. To address these challenges, we propose a Time-aware Knowledge Distillation framework for GRF estimation from insole sensor data. This framework leverages similarity and temporal features within a mini-batch during the knowledge distillation process, effectively capturing the complementary relationships between features and the sequential properties of the target and input data. The performance of the lightweight models distilled through this framework was evaluated by comparing GRF estimations from insole sensor data against measurements from an instrumented treadmill. Empirical results demonstrated that Time-aware Knowledge Distillation outperforms current baselines in GRF estimation from wearable sensor data.

Jisoo Lee, Michael R. Harowicz, Yuwen Chen et al.

This study evaluates publicly available deep-learning based lung segmentation models in transplant-eligible patients to determine their performance across disease severity levels, pathology categories, and lung sides, and to identify limitations impacting their use in preoperative planning in lung transplantation. This retrospective study included 32 patients who underwent chest CT scans at Duke University Health System between 2017 and 2019 (total of 3,645 2D axial slices). Patients with standard axial CT scans were selected based on the presence of two or more lung pathologies of varying severity. Lung segmentation was performed using three previously developed deep learning models: Unet-R231, TotalSegmentator, MedSAM. Performance was assessed using quantitative metrics (volumetric similarity, Dice similarity coefficient, Hausdorff distance) and a qualitative measure (four-point clinical acceptability scale). Unet-R231 consistently outperformed TotalSegmentator and MedSAM in general, for different severity levels, and pathology categories (p<0.05). All models showed significant performance declines from mild to moderate-to-severe cases, particularly in volumetric similarity (p<0.05), without significant differences among lung sides or pathology types. Unet-R231 provided the most accurate automated lung segmentation among evaluated models with TotalSegmentator being a close second, though their performance declined significantly in moderate-to-severe cases, emphasizing the need for specialized model fine-tuning in severe pathology contexts.

Roy Colglazier, Jisoo Lee, Haoyu Dong et al.

The quantity and quality of muscles are increasingly recognized as important predictors of health outcomes. While MRI offers a valuable modality for such assessments, obtaining precise quantitative measurements of musculature remains challenging. This study aimed to develop a publicly available model for muscle segmentation in MRIs and demonstrate its applicability across various anatomical locations and imaging sequences. A total of 362 MRIs from 160 patients at a single tertiary center (Duke University Health System, 2016-2020) were included, with 316 MRIs from 114 patients used for model development. The model was tested on two separate sets: one with 28 MRIs representing common sequence types, achieving an average Dice Similarity Coefficient (DSC) of 88.45%, and another with 18 MRIs featuring less frequent sequences and abnormalities such as muscular atrophy, hardware, and significant noise, achieving 86.21% DSC. These results demonstrate the feasibility of a fully automated deep learning algorithm for segmenting muscles on MRI across diverse settings. The public release of this model enables consistent, reproducible research into the relationship between musculature and health.

Jisoo Lee, Tamim Ahmed, Thanassis Rikakis et al.

Rehabilitation is essential and critical for post-stroke patients, addressing both physical and cognitive aspects. Stroke predominantly affects older adults, with 75% of cases occurring in individuals aged 65 and older, underscoring the urgent need for tailored rehabilitation strategies in aging populations. Despite the critical role therapists play in evaluating rehabilitation progress and ensuring the effectiveness of treatment, current assessment methods can often be subjective, inconsistent, and time-consuming, leading to delays in adjusting therapy protocols. This study aims to address these challenges by providing a solution for consistent and timely analysis. Specifically, we perform temporal segmentation of video recordings to capture detailed activities during stroke patients' rehabilitation. The main application scenario motivating this study is the clinical assessment of daily tabletop object interactions, which are crucial for post-stroke physical rehabilitation. To achieve this, we present a framework that leverages the biomechanics of movement during therapy sessions. Our solution divides the process into two main tasks: 2D keypoint detection to track patients' physical movements, and 1D time-series temporal segmentation to analyze these movements over time. This dual approach enables automated labeling with only a limited set of real-world data, addressing the challenges of variability in patient movements and limited dataset availability. By tackling these issues, our method shows strong potential for practical deployment in physical therapy settings, enhancing the speed and accuracy of rehabilitation assessments.