What’s involved?

Longitudinal Acquisition, Storage and Curation, Interoperability, Reproducibility, Transfer, Anonymization, Security, Privacy, Ethics, 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, HR ...No big deal!

LORIS-CBRAIN INTEGRATION

Benefits vs Challenges

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.”

WHAT IS LORIS?

“..is a modular and extensible web-based data and project management software for neuroimaging research studies. It is an OPEN SOURCE framework and database suitable for managing large datasets.”

Heterogenous data acquisition

Storage, processing & dissemination

What does LORIS do?

What does LORIS do?

Extensible and modular design

LORIS Globally

What does LORIS actually do?

DATA ENTRY
DATA MANAGEMENT
DATA VISUALISATION
DATA QUERYING

TRY ME!

Heterogenous Data

  • Candidate Profile
    •
  • Instrument Builder
    •
  • Feedback Module
    •
  • Double Data Entry
    •
  • Conflict Resolver
    •

Imaging Data

1. Acquisition & Storage

2. Visualisation: Imaging Browser, BrainBrowser

3. Quality Control: Radiological Review Module, DCC MRI

Data Querying

  • Imaging Statistiscs

  • Data Querying Tool (DQT)

What can LORIS do (pointform)

  • Long Term Storage - Large datasets are valuable assets (e.g. ADNI)
  • Anonymity/Privacy - Ethics/IRB compliance and patient confidentiality
  • Data Sharing - Cross project collaborations
  • Secure Web Access- Available through a web browser
  • Heterogeneous Data Management - Single platform for MRI, PET, Clinical & Genetics data
  • Multimodal Data Querying - Easy querying of data, without requiring a programmer
  • Quality Control - Protocol violations, artefact detector, inter-rater reliability
  • Summary Statistics - Demographics, imaging, data entry
  • Processing Platform - Seamless serving of data to processing environments
  • Radiological Reviews - Visualization, including module to curate
  • Import/Export Capabilities - .xls, .csv, etc.
  • Biobanking - Tissue, blood and saliva samples
  • Visualization - 3D and 4D
  • Customizable & Extensible - New modules and features are possible
  • Open Source - Full access to source code. Code is free.

  • 8 year study
  • Longitudinal data
  • 532 subjects
  • 8000 distinct variables
  • 37000 individual assessments
  • T1, T2, PD, DTI
  • Spectroscopy
  • ∼3TB of imaging data
  • 2000 MRI acquisitions

  • Infant brain development in autism
  • 3000+ scans
  • 700+ subjects
  • 7000 distinct variables
  • 150,000+ individual assessments
  • T1, T2, DTI, BOLD
  • ∼5 TBs of imaging data
  • Genetic/biospecimen data

BigBrain

OMEGA

  • Open MEG Archive

  • First open MEG repository

  • 180 user accounts created

  • Associated structural data

  • 500+ reads on academia.edu

MAVAN and the Ludmer Centre

  • MAVAN

  • Maternal Adversity Vulnerability And NeuroDevelopement

  • Behavioral, Imaging and Genomics

  • Key project for the Ludmer Centre

  • Examining acute and chronic stressors on early childhood developement

Open Science

Open Science

Cyberinfrastructure

Open Science

  • Comprises the Biobank and Imaging Centre
  • LORIS is slated the platform for both
  • Data sharing at the MNI will be intergral to research
  • Designed to reduce duplication and make research more efficient

“We’re doing a really shitty job." -- Guy Rouleau

Login

Dashboard

Summary Statistics

LORIS 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

BrainBrowser

..a set of web-based 3D visualization tools primarily used for viewing neurological data i.e. MRI scans.

It allows for real-time manipulation and analysis of 3D neuroimaging data through any modern web browser. TRY ME!

BrainBrowser - 3D Surface Viewer

Protocol Violations

Radiological Review Module

DICOM archives

Imaging Uploader - New

Interactive Protocol Violations - New

Genomics Browser - New

Improved Instrument Builder - New

Configuration module - New

LORIS Roadmap 2016

Easier Installation

DQT integration and improvements

API for imaging

Imaging Browser Enhancements

Documentation - help sections, wikis, code!

Automated Testing

Genomics

QC modules

Better stats

Reduce rependencies - i.e. Quickforms

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

https://github.com/aces/Loris

LORIS - Github Usage

LORIS - Requirements

Dedicated developer! (software is free of charge)

LINUX based server

LAMP stack

Perl and other peripheral libraries (i.e DCMTK)

Beer for Samir

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

How can LORIS be useful to you?

Testimonials

"You don't understand... LORIS saved our lives ... We could share our data anywhere. LORIS makes it really hard to share incorrect data. The quality control data is right there. You can share the QC... it's so well QCed" -- Angelina Paolozza (NeuroDevenet, 2015)

Key Features for the lab

Organize your data

Enable Quality Control

Easy data sharing

Provenance capture

Facilitate image visualization

Summary statistics

Facilitate statistical analysis

Linking your data across modalities

Online Data Querying

Additional Features

Centralized data repository

Download data from one place

Centralized Document Repoistory

Backup your data

Consent is factored in

Anonimyzed automatically online

Raw data can be accessed (e.g. DICOM archiver)

Tablet Friendly - Survey module

Data Sharing Initiatives

Public Data Repositories

Collaborative Data releases

CBRAIN hooks

Ontologicial standardization (e.g. BIDS)

External Provenance (e.g. NIDM)

Interoperability with other competitors

Open Science at the MNI

CCNA Case Example

  • Canadian Consortium for Neurodegeration in Aging

  • Pan Canadian Study

  • $35 million study

  • More than 30 sites

  • Important project for this lab!

Automated PET recognition

Automated PET recognition

Enhanced DICOM anonymization

  • Going dcmtk free -- PYDICOM
  • CONDA
  • Satra knows everything!!

Enhanced DICOM anonymization

Thank you!Acknowledgements: Alan Evans, Alex Zijdenbos, Dario Vins, Jonathan Harlap, Matt Charlet, Andrew Corderey, Sebastian Muehlboeck, Reza Adalat, Louis Collins, Vladimir Fonov, Marc Rousseau, Mia Petkova, Rathi Gnanasekaran, David Brownlee, Tarek Sherif, Pierre Rioux, Nic Kassis, Leigh MacIntyre, Claude Lepage, Ilana Leppert, Natasha Beck, Tristan Glatard, Bert Vincent, Lindsay Lewis, Najma Mahani, Elodie Portales-Casamar, Alden Woodward, Sylvain Milot, Jean Francois Malouin, Sylvain Baillet, Daniel Kroetz, Martin Weiss, Mathieu Desrosier, Jason Karamchandani, Amit Bar-Or, Ted Fon, John Brietner, Derek Lo, Patrick Bermudez, Chris Steele, Pamela Patterson and one of my favourites: Pierre Bellec!

LORIS team on left