Cognition & Circuits

Neuroinformatics and Facilitating Analysis:
Tools, Tips & Tricks

March 28, 2018

Samir Das
Software Manager

McGill Centre for Integrative Neuroscience
Montreal Neurological Institute

Dr. William Feindel

Today's talk

  1. The Basics
  2. Training
  3. Infrastructure
  4. Visualization
  5. Documentation
  6. Best practices in data sharing
  7. Data sharing initiatives
  8. Tools, datasets, and environments
  9. Open Science

Principle #1

Always backup your data!

Principle #2

Learn to Code

Understand Git (and Github)

Principle #3

Learn Statistics

Principle #4

Get involved

Get to know people.
Move outside of your environment.
Socialize.

Principle #5

Be nice!

Projects at the MNI

LORIS globally

  • Cited 295 times
  • Control data for NDAR
  • Longitudinal study (8 years)
  • 532 subjects
  • 8000 distinct variables
  • 37000 individual assessments
  • T1, T2, PD, DTI, Spectroscopy
  • ∼3TB of imaging data
  • 2000 MRI acquisitions

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

CCNA

  • $35 million

  • CIHR funded

  • Pan Canadian Consortium

  • Acquisition in June, 2016

  • 35 collections sites

  • LORIS powered

BigBrain

OMEGA

  • Open MEG Archive

  • First open MEG repository

  • 180 user accounts created

  • Associated structural data

  • 500+ reads on academia.edu

Looking for Volunteer Experience?

Email Leigh MacIntyre -- loris.info@mcin.ca

Training

HBHL

Hackathons

Infrastructure

LORIS - Key features

LORIS Dashboard

LORIS - CBRAIN Data Flow

CBRAIN

CBRAIN projects

cbrain-support.mni@mcgill.ca

CBRAIN tasks

Visualization

BrainBrowser

Validation matters

Documentation

Committee on Best Practices in Data Analysis and Sharing (COBIDAS)

COBIDAS - Key points

  1. Experimental Design
  2. Acquisition Reporting
  3. Preprocessing Reporting
  4. Statistical Modeling and Inference
  5. Results Reporting
  6. Data sharing
  7. Reproducibility

Privacy Concerns

Adrian Thorogood BIC lecture - March 9, 2016

Some Data Sharing solutions?

External Initiatives

INCF, Open Science Framework, NITRC, Allen Institute, NDAR, Open fMRI, Organization Human Brain Mapping, Human Brain Project, Compute Canada, Maelstrom, UK Biobank, Edinburgh BRAINS ImageBank, BRAIN, ENIGMA, Enhanced Nathan Kline Institute (1000 Functional Connectomes), LONI, GAAIN, COINS, XNAT, BrainSpell, VIP, SPM, BrainCode, FSL, FBIRN, Synapse, CIMA-Q, NeuroDevNet, GUSTO, QPN, The NeuroBureau, ABCD...

So many initiatives!

Cuba China Canada Axis

Artificial Intelligence

Consolidated datasets

ADNI, ICBM, NIHPD, Allen Mouse Brain, IBIS, Generation-R, ABIDE, ABIDE Preprocessed, ADHD 200, ADHD Preprocessed, Human Connectome Project, OMEGA, UK Biobank, Edinburgh Biobank, BigBrain, Talairach, 1000 Functional Connectomes, Colin 27, MNI 305, 1000 Brains, AAL, ANIMAL, MAVAN, PreventAD, PING, MNI 152, MNI 305, FSL...

So many datasets!

ADNI

  • Cited 343 times

  • Data-use agreements

  • Used for countless analyses

  • Restrictive

ABIDE

Tools and Environments

Neurovault, NeuroSynth, CIVET, VIP, Boutiques, Git-Annex, SOLID, BIDS, NiDM, DiCAT, DCMTK, NiPype, ITK, Freesurfer, SPM, FSL, Mobile MRI, 1000 Brains, AAL, BrainCode, GitHub, Amazon Cloud, FSL, IDA, BrainVisa, DICOM Confidential, DockerHub, Datalad, Clowdr...

So many Tools!

BIDS

Common Ontology for Imaging Data

NeuroImaging Data Model

Format for storing metadata, provenance, processing information

Neurovault Example

Open Science

What's in it for me?

More citations (Piwowar & Vision, 2013)

Access to larger datasets

Greater exposure

Validation of your data

More collaborations

Increased funding

Free software foundation

Open Science Beers

Wednesdays at 4:44pm

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 (special thanks to Christine Rogers for listening to me.)