Artificial Intelligence with Light Supervision: Application to Neuroimaging

Recent developments in artificial intelligence research have resulted in tremendous success in computer vision, natural language processing and medical imaging tasks, often reaching human or superhuman performance. In this thesis, I further developed artificial intelligence methods based on convolutional neural networks with a special focus on the automated analysis of brain magnetic resonance imaging scans (MRI). I showed that efficient artificial intelligence systems can be created using only minimal supervision, by reducing the quantity and quality of annotations used for training. I applied those methods to the automated assessment of the burden of enlarged perivascular spaces, brain structural changes that may be related to dementia, stroke, mult

Convolutional neural networks for the segmentation of small rodent brain MRI

Image segmentation is a common step in the analysis of preclinical brain MRI, often performed manually. This is a time-consuming procedure subject to inter- and intra- rater variability. A possible alternative is the use of automated, registration-based segmentation, which suffers from a bias owed to the limited capacity of registration to adapt to pathological conditions such as Traumatic Brain Injury (TBI). In this work a novel method is developed for the segmentation of small rodent brain MRI based on Convolutional Neural Networks (CNNs). The experiments here presented show how CNNs provide a fast, robust and accurate alternative to both manual and registration-based methods. This is demonstrated by accurately segmenting three large datasets of MRI scans of healthy and Huntington disease model mice, as well as TBI rats. MU-Net and MU-Net-R, the CCNs here presented, achieve human-level accuracy while eliminating intra-rater variability, alleviating the biases of registration-based segmentation, and with an inference time of less than one second per scan. Using these segmentation masks I designed a geometric construction to extract 39 parameters describing the position and orientation of the hippocampus, and later used them to classify epileptic vs. non-epileptic rats with a balanced accuracy of 0.80, five months after TBI. This clinically transferable geometric approach detects subjects at high-risk of post-traumatic epilepsy, paving the way towards subject stratification for antiepileptogenesis studies

Quantifying Neuromelanin Content Across Varying Magnetic Field Strengths: A Comparative Analysis

Neuromelanin (NM) is an insoluble dark pigment molecule that is found in the substantia nigra of the human brain. Due to its paramagnetic nature, NM can be imaged using MRI in the form of neuromelanin sensitive contrast. This method, known as Neuromelanin Sensitive Magnetic Resonance Imaging (NM-MRI) allows non-invasive imaging of the human substantia nigra through its by-product, NM. NM-MRI research has been mostly done using lower field strength (3 or 1.5 Tesla) MRI scans. The advent of high field strength imaging, e.g., 7 Tesla (7T) provides the opportunity to study neuromelanin production sites with higher spatial resolution and enhanced detail. Since NM-MRI research has not been conducted with high field strength imaging platforms, it is unknown whether the techniques used for quantifying NM at a lower field strength reliably extend to a high field strength platform. In the absence of this information, it is impossible to establish whether these two sequences generate the same estimates of NM. Thus, before it is possible to harness the advantages of high field strength imaging, it is critical to investigate the convergence of NM-MRI signal between 3T and 7T NM-MRI. The current study employs a within-subjects design to answer this question. Neuromelanin sensitive images were obtained from 28 healthy adult participants at both 3T and 7T. NM images were segmented both manually and with the help of a standard atlas. NM in the substantia nigra was quantified in the form of Contrast to Noise Ratio (CNR). Spearman’s rank order correlations assessed statistical dependence between the ranking of participant CNR values at 3T and 7T. We found that CNR values at 3T predicted those at 7T when standard deviation (as opposed to the mean) of the background region was used for defining noise. In addition, CNR values didn’t increase with an increase in field strength. In fact, CNR values at 7T were lower as compared to 3T. This effect was mainly due to a disproportionate increase in noise at 7T. An increased susceptibility noise is a common trade-off for better contrast associated with high field strength imaging. We discuss our findings and comment on the utility of employing high field strength NM- MRI

Neuroimaging at 7 Tesla: a pictorial narrative review

Neuroimaging using the 7-Tesla (7T) human magnetic resonance (MR) system is rapidly gaining popularity after being approved for clinical use in the European Union and the USA. This trend is the same for functional MR imaging (MRI). The primary advantages of 7T over lower magnetic fields are its higher signal-to-noise and contrast-to-noise ratios, which provide high-resolution acquisitions and better contrast, making it easier to detect lesions and structural changes in brain disorders. Another advantage is the capability to measure a greater number of neurochemicals by virtue of the increased spectral resolution. Many structural and functional studies using 7T have been conducted to visualize details in the white matter and layers of the cortex and hippocampus, the subnucleus or regions of the putamen, the globus pallidus, thalamus and substantia nigra, and in small structures, such as the subthalamic nucleus, habenula, perforating arteries, and the perivascular space, that are difficult to observe at lower magnetic field strengths. The target disorders for 7T neuroimaging range from tumoral diseases to vascular, neurodegenerative, and psychiatric disorders, including Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, epilepsy, major depressive disorder, and schizophrenia. MR spectroscopy has also been used for research because of its increased chemical shift that separates overlapping peaks and resolves neurochemicals more effectively at 7T than a lower magnetic field. This paper presents a narrative review of these topics and an illustrative presentation of images obtained at 7T. We expect 7T neuroimaging to provide a new imaging biomarker of various brain disorders

Challenges in Brain Magnetic Resonance Image Segmentation

Over the past several decades, the application of magnetic resonance imaging (MRI) has been rapidly expanding in the areas of brain research studies and clinical diagnosis. One of the most important steps in brain MRI data preparation is the removal of unwanted brain regions, which is followed by segmentation of the brain into three main regions – white matter (WM), grey matter (GM) and cerebrospinal fluid (CSF) – or into subregions. In brain MRI analysis, image segmentation is commonly used for measuring and visualizing the brain’s anatomical structures, analyzing brain changes, delineating pathological regions, and surgical planning and image-guided interventions. Brain segmentation allows clinicians and researchers to concentrate on a specific region in the brain in their analyses. However, brain segmentation is a difficult task due to high similarities and correlations of image intensity among brain regions. In this review, image segmentation algorithms used for dividing the brain into different sectors were discussed in detail. The potential for using the fuzzy c-means (FCM) unsupervised clustering algorithm and certain hybrid (combined) methods to segment brain MR images was demonstrated. Additionally, certain validation techniques that are required to demonstrate the performance of segmentation methods in terms of accuracy rates were described.

Brain Tumor Diagnosis Support System: A decision Fusion Framework

An important factor in providing effective and efficient therapy for brain tumors is early and accurate detection, which can increase survival rates. Current image-based tumor detection and diagnosis techniques are heavily dependent on interpretation by neuro-specialists and/or radiologists, making the evaluation process time-consuming and prone to human error and subjectivity. Besides, widespread use of MR spectroscopy requires specialized processing and assessment of the data and obvious and fast show of the results as photos or maps for routine medical interpretative of an exam. Automatic brain tumor detection and classification have the potential to offer greater efficiency and predictions that are more accurate. However, the performance accuracy of automatic detection and classification techniques tends to be dependent on the specific image modality and is well known to vary from technique to technique. For this reason, it would be prudent to examine the variations in the execution of these methods to obtain consistently high levels of achievement accuracy. Designing, implementing, and evaluating categorization software is the goal of the suggested framework for discerning various brain tumor types on magnetic resonance imaging (MRI) using textural features. This thesis introduces a brain tumor detection support system that involves the use of a variety of tumor classifiers. The system is designed as a decision fusion framework that enables these multi-classifier to analyze medical images, such as those obtained from magnetic resonance imaging (MRI). The fusion procedure is ground on the Dempster-Shafer evidence fusion theory. Numerous experimental scenarios have been implemented to validate the efficiency of the proposed framework. Compared with alternative approaches, the outcomes show that the methodology developed in this thesis demonstrates higher accuracy and higher computational efficiency