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 CBRAIN?


“..is an OPEN SOURCE web-based collaborative High-Performance Computing (HPC) platform for neuroimaging research, connecting researchers to the tools required to handle large datasets.”

What does CBRAIN do?

..enables distributed execution of software pipelines

..aggregates multiple distributed file systems into uniform view

NOW

611 users; 199 international
191 sites
299 countries

CBRAIN Computing Resources

CBRAIN portal

TRY ME!

CBRAIN - Tools

Conversion tools:

MINC ↔ NIfTI, DICOM → MINC, DICOM → NIfTI, Analyze → HRRT, ASPIRO → MINC, DICOM → HRRT, MINC1 ↔ MINC2

Image Processing tools:

  • Civet, CivetCombiner & CivetQC
  • FSL: bedpostx, bet, fast, feat, first flirt, melodic, probtrackx
  • FreeSurfer: recon-all, and recon-all longitudinal
  • NIAK
  • Several other project specific tools

CIVET

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.

Fully automated anatomical pipeline

Parallel processing

Can handle large datasets

Includes QC mechanisms

>10 yrs active development

Publication in process

CIVET - Processing steps

CIVET - Pipeline schema

NIAK

http://niak.simexp-lab.org/

CBRAIN - Functionality

Non-expert users can easily leverage Compute Canada

Anyone can request an account (best effort support):
cbrain-support.mni@mcgill.ca

CBRAIN code is now public: https://github.com/aces/cbrain

Includes several structural and functional MRI tools

Continued integration of new tools as per community needs

MINC

The MINC file format and toolbox was originally conceived, written and released by Peter Neelin in 1992.

Install MINC - BIC systems

By default binaries are available at /usr/local/mni

Better to use /usr/local/bic

A much more up-to-date version is installed in /ipl/quarantine/std/x86_64/1.0

To execute: source /ipl/quarantine/std/x86_64/1.0/init.csh

Install MINC - Personal computers

For personal computers (incl. Macs): https://www.mcgill.ca/bic/resources/minc/minctoolkit

Two versions are mentioned: 1.0 and 1.9.2: install 1.0 version, which includes all the standard MINC tools with support for MINC2.

Main difference: ITK-based software is also included.

MINC resources

CBRAIN GITHUB

https://github.com/aces/cbrain
NITRC: www.nitrc.org/projects/cbrain

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