Ninon Burgos

French National Centre for Scientific Research | CNRS · Institut du Cerveau - ARAMIS Lab

Many studies on machine learning (ML) for computer-aided diagnosis have so far been mostly restricted to high-quality research data. Clinical data warehouses, gathering routine examinations from hospitals, offer great promises for training and validation of ML models in a realistic setting. However, the use of such clinical data warehouses requires...

Purpose: In clinical practice, positron emission tomography (PET) images are mostly analysed visually, but the sensitivity and specificity of this approach greatly depends on the observer’s experience. Quantitative analysis of PET images would alleviate this problem by helping define an objective limit between normal and pathological findings. We p...

In order to reach precision medicine and improve patients’ quality of life, machine learning is increasingly used in medicine. Brain disorders are often complex and heterogeneous, and several modalities such as demographic, clinical, imaging, genetics and environmental data have been studied to improve their understanding. Deep learning, a subpart...

Background and Objective As deep learning faces a reproducibility crisis and studies on deep learning applied to neuroimaging are contaminated by methodological flaws, there is an urgent need to provide a safe environment for deep learning users to help them avoid common pitfalls that will bias and discredit their results. Several tools have been p...

One often lacks sufficient annotated samples for training deep segmentation models. This is in particular the case for less common imaging modalities such as Quantitative Susceptibility Mapping (QSM). It has been shown that deep models tend to fit the target function from low to high frequencies. One may hypothesize that such property can be levera...

Early and accurate diagnosis of parkinsonian syndromes is critical to provide appropriate care to patients and for inclusion in therapeutic trials. The red nucleus is a structure of the midbrain that plays an important role in these disorders. It can be visualized using iron-sensitive magnetic resonance imaging (MRI) sequences. Different iron-sensi...

Reproducibility is a cornerstone of science, as the replication of findings is the process through which they become knowledge. It is widely considered that many fields of science are undergoing a reproducibility crisis. This has led to the publications of various guidelines in order to improve research reproducibility. This didactic chapter intend...

Image synthesis methods in medical and biomedical imaging are able to augment image datasets, increase image resolution, fill missing or incomplete data, derive data in one modality using another modality, prepare perfect annotation, etc. These use cases (and not only those) are mentioned in the second part of this book. The first part of the book...

In this paper, we propose a new method to perform data augmentation in a reliable way in the High Dimensional Low Sample Size (HDLSS) setting using a geometry-based variational autoencoder (VAE). Our approach combines the proposal of 1) a new VAE model, the latent space of which is modeled as a Riemannian manifold and which combines both Riemannian...

Deep learning methods have become very popular for the processing of natural images, and were then successfully adapted to the neuroimaging field. As these methods are non-transparent, interpretability methods are needed to validate them and ensure their reliability. Indeed, it has been shown that deep learning models may obtain high performance ev...

Background Temporary disruption of the blood-brain barrier (BBB) using pulsed ultrasound leads to the clearance of both amyloid and tau from the brain, increased neurogenesis, and mitigation of cognitive decline in pre-clinical models of Alzheimer’s disease (AD) while also increasing BBB penetration of therapeutic antibodies. The goal of this pilot...

Purpose The Centiloid scale provides a systematic means of harmonising amyloid-β PET measures across different acquisition and processing methodologies. This work explores the Centiloid transformation of [ ¹⁸ F]florbetapir PET data acquired on a combined PET/MR scanner and processed with methods that differ from the standard Centiloid pipeline. Me...

Synthetic image data play an important role in the verification of medical and biomedical image analysis algorithms. However, the usage of such data strongly relies on their quality and plausibility. Despite the emergence of many frameworks for image synthesis in recent years, the quality of the generated images has not been sufficiently assessed i...

The contributions of this book demonstrate a wide variety of image synthesis and simulation methods, from parametric modeling to deep learning, and their application to diverse tasks such as image enhancement or data augmentation. The ultimate goal when developing methods is to design a simulation system that can produce realistic anatomical or bio...

This chapter describes how segmentation and registration can be used to synthesize medical images of a particular modality from images of another modality. Segmentation-based approaches can generally be decomposed into two components: the first consists in segmenting the source image and the second consists in assigning intensity values to the diff...

Background: Temporary disruption of the blood-brain barrier (BBB) using pulsed ultrasound leads to the clearance of both amyloid and tau from the brain, increased neurogenesis, and mitigation of cognitive decline in pre-clinical models of Alzheimer’s disease (AD) while also increasing BBB penetration of therapeutic antibodies. The goal of this pilo...

We present Clinica ( www.clinica.run ), an open-source software platform designed to make clinical neuroscience studies easier and more reproducible. Clinica aims for researchers to (i) spend less time on data management and processing, (ii) perform reproducible evaluations of their methods, and (iii) easily share data and results within their inst...

We present Clinica (www.clinica.run), an open-source software platform designed to make clinical neuroscience studies easier and more reproducible. Clinica aims for researchers to i) spend less time on data management and processing, ii) perform reproducible evaluations of their methods, and iii) easily share data and results within their instituti...

In this paper, we propose a new method to perform data augmentation in a reliable way in the High Dimensional Low Sample Size (HDLSS) setting using a geometry-based variational autoencoder. Our approach combines a proper latent space modeling of the VAE seen as a Riemannian manifold with a new generation scheme which produces more meaningful sample...

Many studies on machine learning (ML) for computer-aided diagnosis have so far been mostly restricted to high-quality research data. Clinical data warehouses, gathering routine examinations from hospitals, offer great promises for training and validation of ML models in a realistic setting. However, the use of such clinical data warehouses requires...

Alzheimer’s disease (AD) is characterized by the progressive alterations seen in brain images which give rise to the onset of various sets of symptoms. The variability in the dynamics of changes in both brain images and cognitive impairments remains poorly understood. This paper introduces AD Course Map a spatiotemporal atlas of Alzheimer’s disease...

Diffusion MRI is the modality of choice to study alterations of white matter. In past years, various works have used diffusion MRI for automatic classification of Alzheimer’s disease. However, classification performance obtained with different approaches is difficult to compare because of variations in components such as input data, participant sel...

We performed a systematic review of studies focusing on the automatic prediction of the progression of mild cognitive impairment to Alzheimer’s disease (AD) dementia, and a quantitative analysis of the methodological choices impacting performance. This review included 172 articles, from which 234 experiments were extracted. For each of them, we rep...

This book constitutes the refereed proceedings of the 6th International Workshop on Simulation and Synthesis in Medical Imaging, SASHIMI 2021, held in conjunction with MICCAI 2021, in Strasbourg, France, in September 2021.* The 14 full papers presented were carefully reviewed and selected from 18 submissions. The contributions span the following br...

We ranked third in the Predictive Analytics Competition (PAC) 2019 challenge by achieving a mean absolute error (MAE) of 3.33 years in predicting age from T1-weighted MRI brain images. Our approach combined seven algorithms that allow generating predictions when the number of features exceeds the number of observations, in particular, two versions...

Amyloid PET is a robust biomarker of cortical β‐amyloid accumulation and a candidate endpoint for Alzheimer’s prevention trials. Quantification typically uses Standard Uptake Value Ratio (SUVR) measures acquired over 10‐20 minutes at steady‐state. SUVR may be more susceptible to altered blood flow than modelling of dynamic uptake data from injectio...

This book constitutes the refereed proceedings of the 5th International Workshop on Simulation and Synthesis in Medical Imaging, SASHIMI 2020, held in conjunction with MICCAI 2020, in Lima, Peru, in October 2020. The 19 full papers presented were carefully reviewed and selected from 27 submissions. The contributions span the following broad categor...

We performed a systematic review of studies focusing on the automatic prediction of the progression of mild cognitive impairment to Alzheimer's disease (AD) dementia, and a quantitative analysis of the methodological choices impacting performance. This review included 172 articles, from which 234 experiments were extracted. For each of them, we rep...

Purpose of review: Machine learning is an artificial intelligence technique that allows computers to perform a task without being explicitly programmed. Machine learning can be used to assist diagnosis and prognosis of brain disorders. Although the earliest articles date from more than ten years ago, research increases at a very fast pace. Recent...

Numerous machine learning (ML) approaches have been proposed for automatic classification of Alzheimer's disease (AD) from brain imaging data. In particular, over 30 papers have proposed to use convolutional neural networks (CNN) for AD classification from anatomical MRI. However, the classification performance is difficult to compare across studie...

Deep learning methods have shown a high performance potential for medical image analysis [1], particularly classification for computer-aided diagnosis. However, explaining their decisions is not trivial and could be helpful to achieve better results and know how far they can be trusted. Many methods have been developed in order to explain the decis...

The use of neural networks for diagnosis classification is becoming more and more prevalent in the medical imaging community. However, deep learning method outputs remain hard to explain. Another difficulty is to choose among the large number of techniques developed to analyze how networks learn, as all present different limitations. In this paper,...

In the past two years, over 30 papers have proposed to use convolutional neural network (CNN) for AD classification. However, the classification performances across studies are difficult to compare. Moreover, these studies are hardly reproducible because their frameworks are not publicly accessible. Lastly, some of these papers may reported biased...

Anne Bertrand passed away on March 2nd 2018. She was in a touring-skiers group led by a guide and swept by an avalanche in the French Alps. This paper is a tribute to Anne and an attempt, by some of her closest colleagues, to provide an overview of her major contributions. Anne Bertrand was a rising star of the neuroimaging community who traced inn...

This book constitutes the refereed proceedings of the 4th International Workshop on Simulation and Synthesis in Medical Imaging, SASHIMI 2019, held in conjunction with MICCAI 2019, in Shenzhen, China, in October 2019. The 16 full papers presented were carefully reviewed and selected from 21 submissions. The contributions span the following broad ca...

Diffusion MRI is the modality of choice to study alterations of white matter. In the past years, various works have used diffusion MRI for automatic classification of Alzheimers disease. However, the performances obtained with different approaches are difficult to compare because of variations in components such as input data, participant selection...

We present a fully automatic pipeline for the analysis of PET data on the cortical surface. Our pipeline combines tools from FreeSurfer and PETPVC, and consists of (i) co-registration of PET and T1-w MRI (T1) images, (ii) intensity normalization, (iii) partial volume correction, (iv) robust projection of the PET signal onto the subject's cortical s...

Purpose: Magnetic resonance imaging (MRI)-guided radiation therapy (RT) treatment planning is limited by the fact that the electron density distribution required for dose calculation is not readily provided by MR imaging. We compare a selection of novel synthetic CT generation algorithms recently reported in the literature, including segmentation-...

Pharmacokinetic modelling on dynamic positron emission tomography (PET) data is a quantitative technique. However, the long acquisition time is prohibitive for routine clinical use. Instead, the semi-quantitative standardised uptake value ratio (SUVR) from a shorter static acquisition is used, despite its sensitivity to blood flow confounding longi...

A large number of papers have introduced novel machine learning and feature extraction methods for automatic classification of AD. However, they are difficult to reproduce because key components of the validation are often not readily available. These components include selected participants and input data, image preprocessing and cross-validation...

Owing to its excellent soft-tissue contrast, magnetic resonance (MR) imaging has found an increased application in radiation therapy (RT). Harnessing these properties for treatment planning, automated segmentation methods can alleviate the manual workload burden to the clinical workflow. We investigated atlas-based segmentation methods of organs...

A large number of papers have introduced novel machine learning and feature extraction methods for automatic classification of Alzheimer’s disease (AD). However, while the vast majority of these works use the public dataset ADNI for evaluation, they are difficult to reproduce because different key components of the validation are often not readily...

This book constitutes the refereed proceedings of the Third International Workshop on Simulation and Synthesis in Medical Imaging, SASHIMI 2018, held in conjunction with MICCAI 2018, in Granada, Spain, in September 2018. The 14 full papers presented were carefully reviewed and selected from numerous submissions. This workshop continues to provide a...

We introduce a pipeline for the individual analysis of positron emission tomography (PET) data on large cohorts of patients. This pipeline consists for each individual of generating a subject-specific model of healthy PET appearance and comparing the individual’s PET image to the model via a novel regularised Z-score. The resulting voxel-wise Z-sco...

In recent years, the number of papers on Alzheimer’s disease classification has increased dramatically, generating interesting methodological ideas on the use machine learning and feature extraction methods. However, practical impact is much more limited and, eventually, one could not tell which of these approaches are the most efficient. While ove...

Positron Emission Tomography (PET) with pharmacokinetic (PK) modelling is a quantitative molecular imaging technique, however the long data acquisition time is prohibitive in clinical practice. An approach has been proposed to incorporate blood flow information from Arterial Spin Labelling (ASL) Magnetic Resonance Imaging (MRI) into PET PK modellin...

Background Increasing age is the biggest risk factor for dementia, of which Alzheimer’s disease is the commonest cause. The pathological changes underpinning Alzheimer’s disease are thought to develop at least a decade prior to the onset of symptoms. Molecular positron emission tomography and multi-modal magnetic resonance imaging allow key patholo...

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