Image Processing, Machine Learning and Multimodal Data Analysis
Valentina Pedoia1

1University of California, San Francisco, United States


In this lecture, we provide an overview on the potential of coupling of cutting edge technologies in quantitative MRI, deep learning and big data analytics fields. The main goal is to show how those techniques can be applied to discover latent feature able to accurately characterize disease status and predict progression. The data-driven extraction of features from relaxation maps and multidimensional analysis of data from various sources can exploit the real potential of quantitative MRI technique, to date still hampered by tedious and time-consuming manual image post-processing pipelines; and deeply underused due to the handcrafting of too simplistic image representations.


Quantitative compositional MRI plays a central role in Osteoarthritis(OA) research, offering imaging biomarkers that probe the biochemical composition of the articular cartilage1. While several studies are still limited to analyzing average relaxation time values of manually defined cartilage compartments2, there is growing interest in exploring techniques for the automatic analysis of spatial distribution and extraction of relaxometry patterns able to characterize subjects and predict disease progression. Extraction of second order statistical information, or texture analysis3-5, has been widely used to overcome the limitation of the average ROI-based approaches. However, texture analysis does not address the problem of studying local differences between two groups, and does not allow for the extraction of salient patterns that could characterize cartilage degeneration in a data-driven way. Automation of post-processing pipelines and more effective feature extraction techniques are needed to exploit the real potential of compositional MRI techniques which is, to date, still hampered by tedious and time-consuming manual image post-processing pipelines; and deeply underused due to the handcrafting of overly-simplistic image representations.

Deep Learning applied to MSK Quantitative MRI: Data-Driven Feature Extraction

In the last few years, Computer Vision has been drastically accelerated by the usage of machine learning techniques6-7. With the large availability of annotated data and processing power, supervised learning can today accomplish challenges never demonstrated before using the concepts of transforming data to knowledge by the observation and computational interpretation of said examples8-11. Additionally, a completely new concept has changed the machine-learning field; supervised feature extraction. Conventional machine learning techniques were limited in their ability to process natural data in their raw form. For decades, constructing a pattern-recognition or machine learning system required careful engineering and considerable domain expertise to design feature extractors able to transform raw data, such as the pixel values of an image, into a suitable internal representation or feature vector from which the classifier could detect patterns in the input. In contrast, representation learning allows a machine to be fed with raw data and to automatically discover the best representations of the information hidden in the data needed to accomplish a specified task12. Deep learning neural networks are a representation learning method characterized by the usage of multiple simple, non-linear units to build several interconnected layers. Each layer aggregates the information at increasing levels of abstraction starting with simple image elements, such as edges or contrast, to more complex and semantic aggregations, such as uncovering latent patterns able to accomplish pattern recognition tasks13. The key aspect of deep learning is that these models are not designed to solve a specific task, but are adaptive to the specific problems, learning directly from the data and using a general-purpose learning procedure. Deep learning models were recently applied to solve joint tissues segmentation tasks14-15 and relaxation time feature extraction16-17 showing promising results in overcoming traditional post processing techniques.

Integration and Analysis of Multidimensional Data: Topological Data Analysis to Study OA

While OA is known as a whole joint disease, the data analytics more commonly used are often limited to either univariate analysis or a subset of the variables. However, innovations in the big data analytics field have brought several multidimensional visualization methods with which we can compare individual patients as a ‘point-cloud’ in multidimensional space, overcoming the inherent limitations of single endpoints. One possible approach considers the usage of data shape or topology18. Topological data analysis (TDA) explores relationships between data and data shapes. The fundamental idea of TDA is that this method acts as a geometric approach to pattern recognition within data. By extracting fundamental shapes (patterns) in high-dimensional data TDA provides visualization that can provide novel insights about the data and can identify meaningful sub-groups. Extracting patterns via shape data analysis is possible due to three key ideas: 1) coordinate free description, 2) invariance to small deformations and 3) compactness. The first permits the generalizability of the insights extracted from the shape of complex data. The second guarantees robustness to noise while the last allows complex data to be represented in a simple way. These characteristics make TDA a valuable tool for a combined analysis of all the OA features simultaneously, ultimately leading to a more accurate study of risk factors, pathogenesis and natural history of OA and disease phenotyping19.


In this lecture, recent innovations in the fields of image processing, machine learning and multidimensional/multimodal data analysis to study musculoskeletal disorders will be presented with the aim of discussing the potentials of coupling cutting edge technologies in quantitative compositional MRI and machine learning fields to discover new tools able to automate post-processing, better characterize disease status, and predict progression.


I received funding from NIH-NIAMS K99AR070902 (VP) and GE Healthcare A128218 (SM/VP)


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Proc. Intl. Soc. Mag. Reson. Med. 26 (2018)