Healthy Brains for Healthy Lives - Infrastructure
LORIS, CBRAIN, and more...
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HBHL Steering committee meeting - Demo January 25, 2017 |
What’s involved?
Longitudinal acquisition, storage and curation,
Transfer, Anonymization, Security, Privacy, Ethics
Reproducbility, Interoperability, APIs,
Validation, Quality control, Protocol checking
Preprocessing, Analysis, HPC
Provenance, Ontological standarization, data harmonization
Upgrades, Maintenance, Bug fixes
User Interface, Javascript, Bootstrap
Tracking, Extensibility
Data management, Summary statistics,
Workflows, Development, Tool integration
Data sharing, download, multi-modal linking, querying
Image processing, Visualization,
Networking, System Administration
Partnerships, Funding and HR
...No big deal!
Data flow
What is LORIS?
“LORIS is a modular and extensible web-based data management system that integrates all aspects of a multi-center study: from heterogeneous data acquisition (imaging, clinical, behavior, genetics) to storage, processing and ultimately dissemination.” |
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What does LORIS do?
What does LORIS actually do?
LORIS globally
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BigBrain - high resolution reference brain
Multimodal integration into an anatomically realistic standard space
Years of development
20 micron resolution
7404 histological slices
1 Terabyte dataset
Available freely at https://bigbrain.loris.ca
Open Science
Login
Dashboard
Summary Statistics
Permissions/User control
List of subjects
Timepoints
Battery of Measures
For list of 400+ instruments: https://sites.google.com/site/lorisinstrumentlist
Psychometric Subject Summary
Psychometric Data Entry
Survey Module
Imaging Browser
Imaging Quality Control
Visualization - BrainBrowser
BrainBrowser - 3D Surface Viewer
Protocol Violations
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DICOM archives
Imaging Uploader - New
Data Dictionary Builder
Data Querying Tool
Data Querying Tool - Results
Data Querying Tool - Statistics
Mobile - Responsive layout
Mobile - Data entry
Mobile - Imaging
LORIS - Github - Open Source
LORIS - Requirements for HBHL
Proper resourcing
Reaslitic roadmap
Create use cases
Regular discussions
Beer for Samir
LORIS - Links
Website: www.loris.ca
Demo: https://demo.loris.ca
LORIS developers mailing list: loris-dev@bic.mni.mcgill.ca
Source code: https://github.com/aces/Loris
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Web-based Collaborative research platform Access to remote sources Distributed high performance computing Processing and visualization tools Secure, controlled environment |
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The CIVET project was initiated in order to create an automated, easy-to-use human brain-imaging pipeline that makes use of state-of-the-art software tools developed by researchers at the BIC for the fully-automated processing and analysis of large MR data sets, including the extraction and analysis of cortical surfaces from MR images, as well as many other volumetric and corticometric functions. 
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Fully automated anatomical pipeline Parallel processing Can handle large datasets Includes QC mechanisms 10 yrs active development Publication in process |
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fMRI Pipeline - NIAK
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My name is Pierre Bellec... ... and I love fruit! |
Acknowledgments
Alan Evans, Alex Zijdenbos, Reza Adalat, Penelope Kostopoulos, Louis Collins, Vladimir Fonov, Marc Rousseau, Tarek Sherif, Pierre Rioux, Nic Kassis, Leigh MacIntyre, Claude Lepage, Ilana Leppert, Carolina Makowski, Natasha Beck, Tristan Glatard, Bert Vincent, Lindsay Lewis, Guiomar Niso, Elodie Portales-Casamar, Alden Woodward, Sylvain Milot, Jean Francois Malouin
LORIS Developers: Dario Vins, Jonathan Harlap, Matt Charlet, Andrew Corderey, Sebastien Muehlboeck, David Brownlee, Zia Mohaddes, David MacFarlane, Cecile Madjar, Mia Petkova, Christine Rogers, Rathi Gnanasekeran, Justin Kat, Nicolas Brossard, Tara Campbell, Jordan Stirling, Mouna Safi-Harab, Greg , Rida Abou-Haidar, Daniel Kroetz, Pierre-Emmaunel & Tom Beaudry