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Using Human Connectome Project (HCP) Data

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Baycrest

3560 Bathurst Street

Room 356, Kimel Building 3rd floor

Toronto, ON M6A 2E1

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Workshop Overview:

The Human Connectome Project (HCP) has been the flagship example of large-scale open science in the fields of neuroimaging and cognitive neuroscience for several years. The original HCP Washington University - Minnesota (WU-Minn) corpus is an extremely rich and high-quality repository of brain and behavioural data from multiple imaging modalities (T1-, T2-, Diffusion-weighted MRI; fMRI; MEG) and cognitive domains (memory, motor, language, decision-making, resting-state), from over 1000 healthy young individuals. Extensions into whole-lifespan, developmental, and clinical domains are ongoing, and can be likewise expected to become a major feature of the neuroimaging methodological and scientific ecosystem in the coming years. HCP is an extremely powerful resource for teaching, methods development, exploratory data analysis, and hypothesis testing. However, many researchers are understandably daunted by the mountains of documentation, unwieldy RAM and storage requirements, and novel file formats, pulse sequences, and analysis tools.

This 3-hour hands-on workshop provides a compact overview of the HCP behemoth, introducing attendees to several practical tools and strategies for navigating, accessing, and working with HCP neuroimaging and behavioural data in the context of their own research. It also covers advanced neuroimaging data analysis and visualization tools (CIFTI, connectome workbench), and how these can be deployed in analysis of non-HCP data.

Attendees should bring their own laptops if they wish to undertake the hands-on components of the workshop.

Workshop Objectives:

By the end of this workshop, attendees should:

  • Have gained a broad overview of all imaging, behavioural, and demographic data included in the HCP WU-Minn corpus
  • Be able to browse, search, and download HCP data through both browser-based and command-line tools
  • Have a broad overview of the HCP analysis pipelines code base and how to query + adapt it
  • Have a working practical knowledge of cifti file format and how to incorporate use of cifti files into their analysis pipelines
  • Have gained exposure to connectome workbench software for manipulation and visualization of neuroimaging data
  • Understand how to use the ciftify library to convert their own data to HCP-style cifti file format

In order to follow all hands-on demonstrations, attendees will need IN ADVANCE to:

Workshop Instructors:

Dr. Erin Dickie (PhD, Neurological Sciences, McGill University) is a Project Scientist in the Kimel Family Translational Imaging-Genetics (TIGR) Laboratory at the Centre for Addiction and Mental Health, Toronto, Canada. 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 individualized mapping (PINT), and showed that the brains of those affected by autism are more variable in their organization than those of typically developing controls. Dr. Dickie also assists with the TIGR 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 (https://github.com/edickie/ciftify) that has been publicly available and adopted by international groups.

Dr. John Griffiths (PhD, Cognitive Neuroscience, University of Cambridge) is a Post-doctoral Fellow in the McIntosh Lab at the Rotman Research Institute and in the Lefebvre Lab at the Krembil Research Institute, Toronto Western Hospital. Dr. Griffiths is a core research scientist in the Virtual Brain Consortium, a steering committee member of the RRI Research Training Centre, and an honorary associate at the University of Sydney School of Physics. His research focuses on using personalized connectome-based neural mass and neural field models of large-scale brain dynamics to understand the effects of ageing, neurological disease, and noninvasive brain stimulation. He teaches regularly at domestic and international workshops on the topics of structural and functional neuroimaging methods and computational neuroscience, and has developed software tools for atlas-based querying of white matter tractography connectivity, reproducible research documentation, and spherical harmonic analysis of brain activity patterns.

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Baycrest

3560 Bathurst Street

Room 356, Kimel Building 3rd floor

Toronto, ON M6A 2E1

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