Publications

Pulmonary emphysema is a destructive disease of the lungs that is currently diagnosed via visual assessment of lung Computed Tomography (CT) scans by a radiologist. Visual assessment can have poor inter-rater reliability, is time consuming, and requires access to trained assessors. Quantitative methods that reliably summarize the biologically relevant characteristics of an image are needed to improve the way lung diseases are characterized. The goal of this work was to show how spatial point process models can be used to create a set of radiologically derived quantitative lung biomarkers of emphysema. We formalized a general framework for applying spatial point processes to lung CT scans, and developed a Shot Noise Cox Process to quantify how radiologically based emphysematous tissue clusters into larger structures. Bayesian estimation of model parameters was done using spatial Birth-Death MCMC (BD-MCMC). In simulations, we showed the BD-MCMC estimation algorithm is able to accurately recover model parameters. In an application to real lung CT scans from the COPDGene cohort, we showed variability in the clustering characteristics of emphysematous tissue across disease subtypes that were based on visual assessments of the CT scans.

OBJECTIVE: Deep brain stimulation (DBS) in zona incerta (Zi) is used for symptom alleviation in essential tremor (ET). Zi is positioned along the dentato-rubro-thalamic tract (DRT). Electric field simulations with the finite element method (FEM) can be used for estimation of a volume where the stimulation affects the tissue by applying a fixed isolevel (V). This work aims to develop a workflow for combined patient-specific electric field simulation and white matter tracing of the DRT, and to investigate the influence on the V from different brain tissue models, lead design and stimulation modes. The novelty of this work lies in the combination of all these components.

BACKGROUND: Development of valid, non-invasive biomarkers for parkinsonian syndromes is crucially needed. We aimed to assess whether non-invasive diffusion-weighted MRI can distinguish between parkinsonian syndromes using an automated imaging approach. METHODS: We did an international study at 17 MRI centres in Austria, Germany, and the USA. We used diffusion-weighted MRI from 1002 patients and the Movement Disorders Society Unified Parkinson’s Disease Rating Scale part III (MDS-UPDRS III) to develop and validate disease-specific machine learning comparisons using 60 template regions and tracts of interest in Montreal Neurological Institute space between Parkinson’s disease and atypical parkinsonism (multiple system atrophy and progressive supranuclear palsy) and between multiple system atrophy and progressive supranuclear palsy. For each comparison, models were developed on a training and validation cohort and evaluated in an independent test cohort by quantifying the area under the curve (AUC) of receiving operating characteristic curves. The primary outcomes were free water and free-water-corrected fractional anisotropy across 60 different template regions. FINDINGS: In the test cohort for disease-specific comparisons, the diffusion-weighted MRI plus MDS-UPDRS III model (Parkinson’s disease vs atypical parkinsonism had an AUC 0·962; multiple system atrophy vs progressive supranuclear palsy AUC 0·897) and diffusion-weighted MRI only model had high AUCs (Parkinson’s disease vs atypical parkinsonism AUC 0·955; multiple system atrophy vs progressive supranuclear palsy AUC 0·926), whereas the MDS-UPDRS III only models had significantly lower AUCs (Parkinson’s disease vs atypical parkinsonism 0·775; multiple system atrophy vs progressive supranuclear palsy 0·582). These results indicate that a non-invasive imaging approach is capable of differentiating forms of parkinsonism comparable to current gold standard methods. INTERPRETATIONS: This study provides an objective, validated, and generalisable imaging approach to distinguish different forms of parkinsonian syndromes using multisite diffusion-weighted MRI cohorts. The diffusion-weighted MRI method does not involve radioactive tracers, is completely automated, and can be collected in less than 12 min across 3T scanners worldwide. The use of this test could positively affect the clinical care of patients with Parkinson’s disease and parkinsonism and reduce the number of misdiagnosed cases in clinical trials. FUNDING: National Institutes of Health and Parkinson’s Foundation.

In the last five years, deep learning (DL) has become the state-of-the-art tool for solving various tasks in medical image analysis. Among the different methods that have been proposed to improve the performance of Convolutional Neural Networks (CNNs), one typical approach is the augmentation of the training data set through various transformations of the input image. Data augmentation is typically used in cases where a small amount of data is available, such as the majority of medical imaging problems, to present a more substantial amount of data to the network and improve the overall accuracy. However, the ability of the network to improve the accuracy of the results when a slightly modified version of the same input is presented is often overestimated. This overestimation is the result of the strong correlation between data samples when they are considered independently in the training phase. In this paper, we emphasize the importance of optimizing for accuracy as well as precision among multiple replicates of the same training data in the context of data augmentation. To this end, we propose a new approach that leverages the augmented data to help the network focus on the precision through a specifically-designed loss function, with the ultimate goal to improve both the overall performance and the network’s precision at the same time. We present two different applications of DL (regression and segmentation) to demonstrate the strength of the proposed strategy. We think that this work will pave the way to a explicit use of data augmentation within the loss function that helps the network to be invariant to small variations of the same input samples, a characteristic that is always required to every application in the medical imaging field.

Mastering detailed anatomy of the human deep brain in clinical neurosciences is challenging. Although numerous pioneering works have gathered a large dataset of structural and topographic information, it is still difficult to transfer this knowledge into practice, even with advanced magnetic resonance imaging techniques. Thus, classical histological atlases continue to be used to identify structures for stereotactic targeting in functional neurosurgery. Physicians mainly use these atlases as a template co-registered with the patient’s brain. However, it is possible to directly identify stereotactic targets on MRI scans, enabling personalized targeting. In order to help clinicians directly identify deep brain structures relevant to present and future medical applications, we built a volumetric MRI atlas of the deep brain (MDBA) on a large scale (infra millimetric). Twelve hypothalamic, 39 subthalamic, 36 telencephalic, and 32 thalamic structures were identified, contoured, and labeled. Nineteen coronal, 18 axial, and 15 sagittal MRI plates were created. Although primarily designed for direct labeling, the anatomic space was also subdivided in twelfths of AC-PC distance, leading to proportional scaling in the coronal, axial, and sagittal planes. This extensive work is now available to clinicians and neuroscientists, offering another representation of the human deep brain ([https://hal.archives-ouvertes.fr/] [hal-02116633]). The atlas may also be used by computer scientists who are interested in deciphering the topography of this complex region.

Cerebral microbleeds (CMBs), a common manifestation of mild traumatic brain injury (mTBI), have been sporadically implicated in the neurocognitive deficits of mTBI victims but their clinical significance has not been established adequately. Here we investigate the longitudinal effects of post-mTBI CMBs upon the fractional anisotropy (FA) of white matter (WM) in 21 older mTBI patients across the first  6 months post-injury. CMBs were segmented automatically from susceptibility-weighted imaging (SWI) by leveraging the intensity gradient properties of SWI to identify CMB-related hypointensities using gradient-based edge detection. A detailed diffusion magnetic resonance imaging (dMRI) atlas of WM was used to segment and cluster tractography streamlines whose prototypes were then identified. The correlation coefficient was calculated between (A) FA values at vertices along streamline prototypes and (B) topological (along-streamline) distances between these vertices and the nearest CMB. Across subjects, the CMB identification approach achieved a sensitivity of 97.1% ± 4.7% and a precision of 72.4% ± 11.0% across subjects. The correlation coefficient was found to be negative and, additionally, statistically significant for 12.3% ± 3.5% of WM clusters (p

Radiomics is an emerging field which extracts quantitative radiology data from medical images and explores their correlation with clinical outcomes in a non-invasive manner. This review aims to assess whether radiomics is a useful and reproducible method for clinical management of hepatocellular carcinoma (HCC) by reviewing the strengths and weaknesses of current radiomics literature pertaining specifically to HCC. From an initial set of 48 articles recovered through database searches, 23 articles were retained to be included in this review after full screening. Among these 23 studies, 7 used a radiomics approach in magnetic resonance imaging (MRI). Only two studies applied radiomics to positron emission tomography-computed tomography (PET-CT). In the remaining 14 articles, a radiomics analysis was performed on computed tomography (CT). Eight studies dealt with the relationship between biological signatures and imaging findings, and can be classified as radiogenomic studies. For each study included in our review, we computed a Radiomics Quality Score (RQS) as proposed by Lambin et al. We found that the RQS (mean ± standard deviation) was 8.35 ± 5.38 (out of a possible maximum value of 36). Although these scores are fairly low, and radiomics has not yet reached clinical utility in HCC, it is important to underscore the fact that these early studies pave the way for the radiomics field with a focus on HCC. Radiomics is still a very young field, and is far from being mature, but it remains a very promising technology for the future for developing adequate personalized treatment as a non-invasive approach, for complementing or replacing tumor biopsies, as well as for developing novel prognostic biomarkers in HCC patients.

The present survey describes the state-of-the-art techniques for dynamic cardiac magnetic resonance image reconstruction. Additionally, clinical relevance, main challenges, and future trends of this image modality are outlined. Thus, this paper aims to provide a general vision about cine MRI as the standard procedure in functional evaluation of the heart, focusing on technical methodologies.