A bayesian approach to examining default mode network functional connectivity and cognitive performance in major depressive disorder.

To reconcile the inconsistency of the association between the resting-state functional connectivity (RSFC) and cognitive performance in healthy and depressed groups due to high variance of both measures, we proposed a Bayesian spatio-temporal model to precisely and accurately estimate the RSFC in depressed and nondepressed participants. This model was employed to estimate spatially-adjusted functional connectivity (saFC) in the extended default mode network (DMN) that was hypothesized to correlate with cognitive performance in both depressed and nondepressed. Multiple linear regression models were used to study the relationship between DMN saFC and cognitive performance scores measured in the following four cognitive domains while adjusting for age, sex, and education.

Cerebrospinal fluid biomarkers of neurodegeneration, synaptic dysfunction, and axonal injury relate to atrophy in structural brain regions specific to Alzheimer's disease.

Introduction: Patterns of atrophy can distinguish normal cognition from Alzheimer's disease (AD), but neuropathological drivers of this pattern are unknown. This study examined associations between cerebrospinal fluid biomarkers of AD pathology, synaptic dysfunction, and neuroaxonal injury with two AD imaging signatures.

Methods: Signatures were calculated using published guidelines.

Structural Correlates of the Sensorimotor Cerebellum in Parkinson's Disease and Essential Tremor.

Background: Parkinson's disease (PD) and essential tremor (ET) are commonly encountered movement disorders. Pathophysiologic processes that localize to the cerebellum are described in both. There are limited studies investigating cerebellar structural changes in these conditions, largely because of inherent challenges in the efficiency of segmentation.

Assessing the Accuracy of a Deep Learning Method to Risk Stratify Indeterminate Pulmonary Nodules.

The management of indeterminate pulmonary nodules (IPNs) remains challenging, resulting in invasive procedures and delays in diagnosis and treatment. Strategies to decrease the rate of unnecessary invasive procedures and optimize surveillance regimens are needed. To develop and validate a deep learning method to improve the management of IPNs.

Hippocampal activation and connectivity in the aging brain.

The hippocampus and underlying cortices are highly susceptible to pathologic change with increasing age. Using an associative face-scene (Face-Place) encoding task designed to target these regions, we investigated activation and connectivity patterns in cognitively normal older adults. Functional MRI scans were collected in 210 older participants (mean age = 76.

Thalamocortical Anatomical Connectivity in Schizophrenia and Psychotic Bipolar Disorder.

Background: Anatomical connectivity between the thalamus and cortex, including the prefrontal cortex (PFC), is abnormal in schizophrenia. Overlapping phenotypes, including deficits in executive cognitive abilities dependent on PFC-thalamic circuitry, suggest dysrupted thalamocortical anatomical connectivity may extend to psychotic bipolar disorder. We tested this hypothesis and examined the impact of illness stage to inform when in the illness course thalamocortical dysconnectivity emerges.

LEARNING 3D WHITE MATTER MICROSTRUCTURE FROM 2D HISTOLOGY.

Histological analysis is typically the gold standard for validating measures of tissue microstructure derived from magnetic resonance imaging (MRI) contrasts. However, most histological investigations are inherently 2-dimensional (2D), due to increased field-of-view, higher in-plane resolutions, ease of acquisition, decreased costs, and a large number of available contrasts compared to 3-dimensional (3D) analysis. Because of this, it would be of great interest to be able to learn the 3D tissue microstructure from 2D histology.

Deep Learning Estimation of Multi-Tissue Constrained Spherical Deconvolution with Limited Single Shell DW-MRI.

Diffusion-weighted magnetic resonance imaging (DW-MRI) is the only non-invasive approach for estimation of intra-voxel tissue microarchitecture and reconstruction of in vivo neural pathways for the human brain. With improvement in accelerated MRI acquisition technologies, DW-MRI protocols that make use of multiple levels of diffusion sensitization have gained popularity. A well-known advanced method for reconstruction of white matter microstructure that uses multi-shell data is multi-tissue constrained spherical deconvolution (MT-CSD).

Harmonizing 1.5T/3T Diffusion Weighted MRI through Development of Deep Learning Stabilized Microarchitecture Estimators.

Diffusion weighted magnetic resonance imaging (DW-MRI) is interpreted as a quantitative method that is sensitive to tissue microarchitecture at a millimeter scale. However, the sensitization is dependent on acquisition sequences (e.g.

Contrast Phase Classification with a Generative Adversarial Network.

Dynamic contrast enhanced computed tomography (CT) is an imaging technique that provides critical information on the relationship of vascular structure and dynamics in the context of underlying anatomy. A key challenge for image processing with contrast enhanced CT is that phase discrepancies are latent in different tissues due to contrast protocols, vascular dynamics, and metabolism variance. Previous studies with deep learning frameworks have been proposed for classifying contrast enhancement with networks inspired by computer vision.

Semi-supervised Machine Learning with MixMatch and Equivalence Classes.

Semi-supervised methods have an increasing impact on computer vision tasks to make use of scarce labels on large datasets, yet these approaches have not been well translated to medical imaging. Of particular interest, the MixMatch method achieves significant performance improvement over popular semi-supervised learning methods with scarce labels in the CIFAR-10 dataset. In a complementary approach, Nullspace Tuning on equivalence classes offers the potential to leverage multiple subject scans when the ground truth for the subject is unknown.

CircleNet: Anchor-free Glomerulus Detection with Circle Representation.

Object detection networks are powerful in computer vision, but not necessarily optimized for biomedical object detection. In this work, we propose CircleNet, a simple anchor-free detection method with circle representation for detection of the ball-shaped glomerulus. Different from the traditional bounding box based detection method, the bounding circle (1) reduces the degrees of freedom of detection representation, (2) is naturally rotation invariant, (3) and optimized for ball-shaped objects.

Generalizing Deep Whole Brain Segmentation for Pediatric and Post- Contrast MRI with Augmented Transfer Learning.

Generalizability is an important problem in deep neural networks, especially in the context of the variability of data acquisition in clinical magnetic resonance imaging (MRI). Recently, the Spatially Localized Atlas Network Tiles (SLANT) approach has been shown to effectively segment whole brain non-contrast T1w MRI with 132 volumetric labels. Enhancing generalizability of SLANT would enable broader application of volumetric assessment in multi-site studies.

Semi-Supervised Multi-Organ Segmentation through Quality Assurance Supervision.

Human in-the-loop quality assurance (QA) is typically performed after medical image segmentation to ensure that the systems are performing as intended, as well as identifying and excluding outliers. By performing QA on large-scale, previously unlabeled testing data, categorical QA scores (e.g.

MRI correlates of chronic symptoms in mild traumatic brain injury.

Some veterans with a history of mild traumatic brain injury (mTBI) have reported experiencing auditory and visual dysfunction that persist beyond the acute phase of the incident. The etiology behind these symptoms is difficult to characterize, since mTBI is defined by negative imaging findings on current clinical imaging. There are several competing hypotheses that could explain functional deficits; one example is shear injury, which may manifest in diffusion-weighted magnetic resonance (MR) imaging (DWI).

Validation and Optimization of Multi-Organ Segmentation on Clinical Imaging Archives.

Segmentation of abdominal computed tomography (CT) provides spatial context, morphological properties, and a framework for tissue-specific radiomics to guide quantitative Radiological assessment. A 2015 MICCAI challenge spurred substantial innovation in multi-organ abdominal CT segmentation with both traditional and deep learning methods. Recent innovations in deep methods have driven performance toward levels for which clinical translation is appealing.

Deep Multi-task Prediction of Lung Cancer and Cancer-free Progression from Censored Heterogenous Clinical Imaging.

Annual low dose computed tomography (CT) lung screening is currently advised for individuals at high risk of lung cancer (e.g., heavy smokers between 55 and 80 years old).

Extracting 2D weak labels from volume labels using multiple instance learning in CT hemorrhage detection.

Multiple instance learning (MIL) is a supervised learning methodology that aims to allow models to learn instance class labels from bag class labels, where a bag is defined to contain multiple instances. MIL is gaining traction for learning from weak labels but has not been widely applied to 3D medical imaging. MIL is well-suited to clinical CT acquisitions since (1) the highly anisotropic voxels hinder application of traditional 3D networks and (2) patch-based networks have limited ability to learn whole volume labels.

Internal-transfer Weighting of Multi-task Learning for Lung Cancer Detection.

Deep learning has achieved many successes in medical imaging, including lung nodule segmentation and lung cancer prediction on computed tomography (CT). Recently, multi-task networks have shown to both offer additional estimation capabilities, and, perhaps more importantly, increased performance over single-task networks on a "main/primary" task. However, balancing the optimization criteria of multi-task networks across different tasks is an area of active exploration.

Outlier Guided Optimization of Abdominal Segmentation.

Abdominal multi-organ segmentation of computed tomography (CT) images has been the subject of extensive research interest. It presents a substantial challenge in medical image processing, as the shape and distribution of abdominal organs can vary greatly among the population and within an individual over time. While continuous integration of novel datasets into the training set provides potential for better segmentation performance, collection of data at scale is not only costly, but also impractical in some contexts.

Using deep learning for a diffusion-based segmentation of the dentate nucleus and its benefits over atlas-based methods.

The dentate nucleus (DN) is a gray matter structure deep in the cerebellum involved in motor coordination, sensory input integration, executive planning, language, and visuospatial function. The DN is an emerging biomarker of disease, informing studies that advance pathophysiologic understanding of neurodegenerative and related disorders. The main challenge in defining the DN radiologically is that, like many deep gray matter structures, it has poor contrast in T1-weighted magnetic resonance (MR) images and therefore requires specialized MR acquisitions for visualization.

Cortical Surface Parcellation using Spherical Convolutional Neural Networks.

We present cortical surface parcellation using spherical deep convolutional neural networks. Traditional multi-atlas cortical surface parcellation requires inter-subject surface registration using geometric features with slow processing speed on a single subject (2-3 hours). Moreover, even optimal surface registration does not necessarily produce optimal cortical parcellation as parcel boundaries are not fully matched to the geometric features.

Discovering novel disease comorbidities using electronic medical records.

Increasing reliance on electronic medical records at large medical centers provides unique opportunities to perform population level analyses exploring disease progression and etiology. The massive accumulation of diagnostic, procedure, and laboratory codes in one place has enabled the exploration of co-occurring conditions, their risk factors, and potential prognostic factors. While most of the readily identifiable associations in medical records are (now) well known to the scientific community, there is no doubt many more relationships are still to be uncovered in EMR data.

Stochastic tissue window normalization of deep learning on computed tomography.

Tissue window filtering has been widely used in deep learning for computed tomography (CT) image analyses to improve training performance (e.g., soft tissue windows for abdominal CT).

Reproducibility Evaluation of SLANT Whole Brain Segmentation Across Clinical Magnetic Resonance Imaging Protocols.

Whole brain segmentation on structural magnetic resonance imaging (MRI) is essential for understanding neuroanatomical-functional relationships. Traditionally, multi-atlas segmentation has been regarded as the standard method for whole brain segmentation. In past few years, deep convolutional neural network (DCNN) segmentation methods have demonstrated their advantages in both accuracy and computational efficiency.