Seminar – Benjamin de Leener

SEMINAR UNF SERIES Speaker: Benjamin De Leener, Ph.D. Title: The MRI anatomy of the spinal cord, Part I  Where: CRIUGM Room E1910 (http://www.criugm.qc.ca/en/contact.html) When: Thursday June 7th,  13h-14h *The seminar will be presented in English Benjamin De Leener (PhD) is a HBHL Postdoctoral Fellow at Doyon Lab). He has a strong passion for medical imaging technologies and computer vision in general. Being able to understand and utilize the content of an image has the potential to revolutionize the way we interact with the world. His main contribution is the development of the Spinal Cord Toolbox (SCT), a comprehensive and open-source software for analyzing MRI images of the spinal cord. SCT includes tools for automatically detecting and segmenting spinal cord structures and extracting multi-parametric MRI data from white matter pathways and gray matter sub regions. His research interests are the development of new analysis and processing methods for medical data, with a particular interest in MRI and neurosciences. Abstract: Over the last decade, the neuroimaging community has developed various tools for processing and analyzing MRI data of the spinal cord. Particularly, recent advances in MRI templates of the spinal cord allows unbiased multicentric studies of large groups of patients, by providing a common referential space. However, the coordinate systems used to build these templates and atlases are based on anatomical structure (a.k.a. the vertebral bodies) and do not appropriately represent the functions of the spinal cord, therefore leading to potential errors when analyzing functional MRI data or the spinal cord internal structure (gray/white matter). This study presents a novel approach for approximating the position of the spinal roots along the...

Seminar – Anisha Keshavan

SEMINAR UNF SERIES Speaker: Dr Anisha Keshavan Title: Leveraging Web Technology to address challenges with Big Data in Neuroscience.  Where: CRIUGM Room E1910 (http://www.criugm.qc.ca/en/contact.html) When: Thursday May 31st,  13h-14h *The seminar will be presented in English Dr Anisha Keshavan works with Jason Yeatman in Speech and Hearing Sciences and Ariel Rokem at the eScience Institute. Her research focuses on big data methods in neuroimaging. Advances in MRI technology and image segmentation algorithms have enabled researchers to begin to understand the mechanisms of healthy brain development, psychiatric and neurological disorders. However, accurately measuring the brain at a scale large enough to accommodate genetic association and precision medicine studies is challenging; expert neuroanatomist tracings can take a long time, while automated algorithms are not accurate enough. Dr Keshavan aims to develop methods to combine the accuracy of an experts with the speed of computers by incorporating crowdsourced image segmentation with deep learning algorithms. She received a doctoral degree in Bioengineering from the UC Berkeley – UCSF Joint Graduate Program, and a Bachelor’s degree in Aerospace Engineering and Applied Mathematics from the University of California, Los Angeles. Abstract: Advances in technology have enabled neuroscientists to collect massive amounts of data to answer important scientific questions. But the drawback is that we are experiencing a “data deluge”, which has brought about new challenges that we must overcome in order to truly reap the benefits that Big Data promises. In this talk, I propose that web technology can help us overcome big data challenges, and present examples of how this is done in the field of neuroimaging. First, how web-based data visualization can address...

Seminar – Erin W. Dickie

SEMINAR UNF SERIES Speaker: Dr Erin W. Dickie Title: Personalized Connectomics for the Study of Brain Health and Disease: Applications to Autism Spectrum Disorder and Schizophrenia Research. Where: CRIUGM Room E1910 (http://www.criugm.qc.ca/en/contact.html) When: Thursday May 24th,  13h-14h *The seminar will be presented in English Dr. Erin Dickie (PhD, Neurological Sciences, McGill University) is a Project Scientist. Dr. Dickie’s research focus is personalized connectomics, or the ability to map brain organization at the level of the individual. Individual mapping of brain function may be a critical first step in the design of targets for stimulation therapy. Dr. Dickie recently submitted a manuscript describing her tool for mapping neurodiversity (PINT), and showed that the brains of those affected by autism and more variable in their organization that those of typically developing controls. This work suggests that personalized brain mapping might be a critical first step for future biomarker discovery. Dr. Dickie also assists with the lab’s data management and analysis system, and builds automated tools for data analysis. In the past year, she has developed a new tool for surface-based analyses (ciftify) that has been publicly available and adopted by international groups. Abstract: Emerging work from the neuroimaging community shows that everyone’s cerebral cortex has a unique functionally organisation and that this unique organisation can be mapped using neuroimaging data at the individual participant level. To do so, we start with an analytic approach, using the CIFTI file format, that allows for a more neuroanatomically-faithful representation of data. An open source set of tools ‘ciftify’ (https://edickie.github.io/ciftify) make this approach more accessible to the greater scientific community. We than introduce novel methods...

Seminar – Tal Yarkoni

SEMINAR UNF SERIES Speaker: Dr Tal Yarkoni Title: How to survive and thrive as an open scientist Where: CRIUGM Amphithéâtre Le Groupe Maurice (http://www.criugm.qc.ca/en/contact.html) When: Thursday May 17th,  13h-14h *The seminar will be presented in English Dr Yarkoni is a Research Assistant Professor in the Department of Psychology at the University of Texas, where he directs the Psychoinformatics Lab. His research focuses on the development and application of new methods for acquiring, organizing, and synthesizing psychological data on a large scale. Tal’s work applies techniques from behavioral psychology, functional neuroimaging, and computer science to multiple domains within psychology, with a particular focus on personality and individual differences. Abstract: In principle, science is a cumulative, community-driven enterprise. To make new discoveries, researchers build directly on the products of other researchers’ efforts, and in turn, reciprocally share their own findings with the world. In practice, of course, things rarely proceed quite so idealistically. Researchers regularly hide their latest findings from one another as they compete for publication in rarified journals; data and protocols are hoarded to maintain competitive advantage; and “Questionable Research Practices” such as optional stopping and selective reporting are engaged in with alarming frequency, often under the justification that there is no other way for a modern scientist to succeed. In this talk I take issue with this philosophy, and argue that it is indeed possible for an open scientist to both survive and thrive in the modern environment. I review a series of open practices that can help advance one’s career while simultaneously maximizing the reproducibility, reliability, and accessibility of one’s scientific work. These include preprint deposition, open-access publication, preregistration, version...