diff --git a/CBRAIN_indepth.html b/CBRAIN_indepth.html index 9fc4e5a..7b9b8ac 100755 --- a/CBRAIN_indepth.html +++ b/CBRAIN_indepth.html @@ -4,7 +4,7 @@ - LORIS - A Database System + CBRAIN @@ -34,45 +34,12 @@
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+ +
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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! -

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LORIS-CBRAIN INTEGRATION

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Benefits vs Challenges

- -
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- - +
@@ -94,57 +61,123 @@

LORIS-CBRAIN INTEGRATION

+ +
+

CBRAIN orchestrates large amounts
of data and computation running
on remote supercomputing resources.
+
+ In other words, it makes big science
easier, manageable, and more reliable!

+ +
+
- + + +
-

What does CBRAIN do?

+

What does
CBRAIN do?

-

..enables distributed execution of software pipelines

 +

..enables distributed execution
of software pipelines
-

..aggregates multiple distributed file systems into uniform view

+

..aggregates multiple distributed
file systems into uniform view

- - -
- + +
+
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-

NOW

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611 users; 199 international
- 191 sites
- 299 countries

+ +
+

How does CBRAIN Work?

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+ +
+ +
+ +
+ +
+ +
+ +

More Info at: http://boutiques.github.io/

+

Contribute on Github: https://github.com/boutiques/boutiques +

+
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+ +
+ +
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+ +
+ +
+ +
+ + + +
+

What can CBRAIN
do for you?

+
    +
  • Convenient and secure web access (no software installation required)
    • +
  • Distributed storage with automated, multipoint data movement, and cataloging +
    • +
  • Transparent access to research tools and computing (HPC and cloud)
    • +
  • Flexibility to adapt to extremely heterogeneous computing and data sites
    • +
  • Full audit trail (data provenance) and logs across all user actions
    • +
  • Lightweight core components, low requirements for deployment and operation
    • +
  • Scalability (no architectural bottlenecks)
    • +
  • Maintainability and sustainability by a research-based team
    • +
  • Full ecosystem security and monitoring
    •  +
+
+
+ + +
+
+

Who uses CBRAIN?

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CBRAIN Computing Resources

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+ +
+ +
+

CBRAIN Computational Resources
provided by Compute Canada

+ +

~7 million CPU hours per year up to 8 PB of Storage

+ +
- + +

CBRAIN portal

TRY ME!

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+
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+ +
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CBRAIN - Tools

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Conversion tools:

+

Conversion tools:

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

-

Image Processing tools: +

Image Processing tools:

  • Civet, CivetCombiner & CivetQC
  • FSL: bedpostx, bet, fast, feat, first flirt, melodic, probtrackx
    • @@ -164,12 +197,12 @@

    CIVET

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    Fully automated anatomical pipeline

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    Parallel processing

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    Can handle large datasets

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    Includes QC mechanisms

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    >10 yrs active development

    -

    Publication in process

    +

    Fully automated anatomical pipeline

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    Parallel processing

    +

    Can handle large datasets

    +

    Includes QC mechanisms

    +

    >10 yrs active development

    +

    Publication in process

@@ -200,75 +233,30 @@

CIVET - Pipeline schema

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NIAK

-

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

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NIAK

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Another imaging pipeline

- -
+

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

+

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

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MINC

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

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Install MINC - BIC systems

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

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Better to use /usr/local/bic

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

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

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- -
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Install MINC - Personal computers

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

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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.

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Main difference: ITK-based software is also included.

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MINC resources

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+

CBRAIN GITHUB

-

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

+

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

- +
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