diff --git a/LORIS_indepth.html b/LORIS_indepth.html index aeecf07..3e6f38b 100755 --- a/LORIS_indepth.html +++ b/LORIS_indepth.html @@ -33,74 +33,15 @@
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What’s involved?

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- 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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WHAT IS LORIS?

 @@ -111,22 +52,10 @@

LORIS-CBRAIN INTEGRATION

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WHAT IS LORIS?

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“..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.”

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Heterogenous data acquisition

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Heterogenous data acquisition

Storage, processing & dissemination
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A flexible, customizable, and open source neuroimaging
database suitable for multiple types of projects.

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What does LORIS do?

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LORIS Around the World!

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What does LORIS
actually do?

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What does LORIS do?

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What does LORIS do?

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Data Entry
Data Management
Data Visualization
Data Querying

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Try the
LORIS Demo

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What can LORIS
do for you?

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

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...follow along at: Follow along at: demo.loris.ca


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Or click the image below

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Dashboard

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Summary Statistics

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Permissions/User control

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List of subjects

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Timepoints

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Battery of Measures

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For list of 400+ instruments: https://sites.google.com/site/lorisinstrumentlist + +

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Psychometric
Subject Summary

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Psychometric
Data Entry

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Survey Module

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Extensible and modular design

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See more key LORIS features below

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Extensible and
modular design

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Extensible and modular design

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LORIS Globally

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What does LORIS actually do?

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- DATA ENTRY
- DATA MANAGEMENT
- DATA VISUALISATION
- DATA QUERYING
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TRY ME!

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Heterogenous Data

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

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Imaging Data

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1. Acquisition & Storage

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2. Visualisation: Imaging Browser, BrainBrowser

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3. Quality Control: Radiological Review Module, DCC MRI

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2. Visualisation:Imaging Browser, BrainBrowser

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3. Quality Control: Radiological Review Module,
DCC MRI

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Data Querying

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Data Querying

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  • Imaging Statistiscs

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  • Data Querying Tool (DQT)

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  • Data Querying Tool (DQT)

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General Statistics

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Imaging Statistics

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Imaging Browser

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Imaging Quality Control

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BrainBrowser

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

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

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BrainBrowser
3D Surface Viewer

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Protocol Violations

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Radiological
Review Module

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DICOM archives

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Imaging Uploader

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Interactive Protocol Violations

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Genomics Browser

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Improved Instrument Builder

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Configuration module

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Automated PET recognition

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Automated PET recognition

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Enhanced DICOM anonymization

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    +
  • Going dcmtk free -- PYDICOM
    • +
  • CONDA
    • +
  • Satra knows everything!!
    • +
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Enhanced DICOM anonymization

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+ [PLACEHOLDER] +

Electrophysiology Browser for EEG

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+ [PLACEHOLDER] +

Automated pipelines for BIDS format data

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Data Querying Tool (DQT)
...it's pretty cool!

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Data Dictionary Builder

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Data Querying Tool

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Data Querying Tool Results

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Data Querying Tool Statistics

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LORIS has some other
cool features...

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Mobile - Responsive layout

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Mobile - Data entry

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Mobile - Imaging

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What can LORIS do (pointform)

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    -
  • 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.
    • -
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LORIS is freely available on GitHub - fully Open Source

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https://github.com/aces/Loris

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LORIS - Github Usage

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LORIS is used across the globe

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Discover studies that use LORIS below

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What can LORIS do (pointform)

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BigBrain

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BigBrain

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What can LORIS do (pointform)
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OMEGA

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  • Open MEG Archive

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  • First open MEG repository

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  • 180 user accounts created

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  • Associated structural data

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  • 500+ reads on academia.edu

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Open MNI iEEG atlas

+ [Christine to add content] +
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MAVAN and the Ludmer Centre

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MAVAN and the Ludmer Centre

  • Behavioral, Imaging and Genomics

  • Key project for the Ludmer Centre

  • Examining acute and chronic stressors on early childhood developement

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    LORIS is just one part of the MNI Ecosystem
    contributing to Open Science

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    Open Science

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    MAVAN and the Ludmer Centre

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    +

    What’s involved?

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    + 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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    Open Science

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    Cyberinfrastructure

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    WHAT IS CBRAIN?

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    Open Science

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    • Comprises the Biobank and Imaging Centre
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    • LORIS is slated the platform for both
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    • Data sharing at the MNI will be intergral to research
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    • Designed to reduce duplication and make research more efficient
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    “We’re doing a really shitty job." -- Guy Rouleau

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    Login

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    Dashboard

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    Summary Statistics

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    LORIS summary statistics

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    Permissions/User control

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    List of subjects

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    Timepoints

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    Battery of Measures

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    For list of 400+ instruments: https://sites.google.com/site/lorisinstrumentlist - -

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    Psychometric Subject Summary

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    Psychometric Data Entry

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    Survey Module

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    Imaging Browser

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    Imaging Quality Control

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    BrainBrowser

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    ..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!

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    - + + + - -
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    “..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.”

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    More on CBRAIN *HERE - link to cbrain pres*

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    BrainBrowser - 3D Surface Viewer

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    Protocol Violations

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    Radiological Review Module

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    DICOM archives

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    Imaging Uploader - New

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    Interactive Protocol Violations - New

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    Genomics Browser - New

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    Improved Instrument Builder - New

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    Configuration module - New

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    LORIS Roadmap 2016

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    Easier Installation

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    DQT integration and improvements

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    API for imaging

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    Imaging Browser Enhancements

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    Documentation - help sections, wikis, code!

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    Automated Testing

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    Genomics

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    QC modules

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    Better stats

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    Reduce rependencies - i.e. Quickforms

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    Data Dictionary Builder

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    Data Querying Tool

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    Data Querying Tool - Results

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    Data Querying Tool - Statistics

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    Mobile - Responsive layout

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    Mobile - Data entry

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    Mobile - Imaging

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    LORIS - Github - Open Source

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    https://github.com/aces/Loris

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    LORIS - Github Usage

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    LORIS - Requirements

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    LORIS-CBRAIN INTEGRATION

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    LORIS - Requirements

    Dedicated developer! (software is free of charge)

    LINUX based server

    LAMP stack

    Perl and other peripheral libraries (i.e DCMTK)

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    Beer for Samir

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    LORIS - Requirements for HBHL

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    Scaling LORIS
    Institutions and Consortia

    Proper resourcing

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    Reaslitic roadmap

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    Realistic roadmap

    Create use cases

    Regular discussions

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    Beer for Samir

    LORIS - Links

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    Website: www.loris.ca

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    Demo: https://demo.loris.ca

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    LORIS developers mailing list: loris-dev@bic.mni.mcgill.ca

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    Source code: https://github.com/aces/Loris

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    Website:
    www.loris.ca

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    Demo:
    https://demo.loris.ca

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    LORIS developers mailing list:
    loris-dev@bic.mni.mcgill.ca

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    Source code:
    https://github.com/aces/Loris

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    How can LORIS be useful to you?

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    How can LORIS be
    useful to you?

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    Testimonials

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    "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)

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    Testimonials

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    "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. We analyzed and published our results two years earlier than it would have taken without LORIS." -- Angelina Paolozza, PhD student (NeuroDevNet, 2015)

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    Key Features for the lab

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    Organize your data

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    Enable Quality Control

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    Easy data sharing

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    Provenance capture

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    Facilitate image visualization

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    Summary statistics

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    Facilitate statistical analysis

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    Linking your data across modalities

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    Online Data Querying

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    Additional Features

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    Centralized data repository

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    Download data from one place

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    Centralized Document Repoistory

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    Backup your data

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    Consent is factored in

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    Anonimyzed automatically online

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

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    Tablet Friendly - Survey module

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    Key Features for the Lab

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    • Organize your data!
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    • Quality Control
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    • Easy data sharing
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    • Provenance capture
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    • Facilitate image visualization
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    • Summary statistics
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    • Facilitate statistical analysis
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    +     		+
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    • Linking your data across modalities
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    • Online Data Querying
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    • Centralized document repository
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    • >Data backup
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    • Consent is factored in
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    • Anonimyzed automatically online
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    • Raw data can be accessed (e.g. DICOM archiver)
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    Data Sharing Initiatives

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    Public Data Repositories

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    Collaborative Data releases

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    CBRAIN hooks

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    Ontologicial standardization (e.g. BIDS)

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    External Provenance (e.g. NIDM)

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    Interoperability with other competitors

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    Open Science at the MNI

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    Data Sharing Initiatives

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    • Public Data Repositories
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    • Collaborative Data releases
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    • CBRAIN hooks
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    • Ontologicial standardization (e.g. BIDS)
      • +
    • External Provenance (e.g. NIDM)
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    • Interoperability with other competitors
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    • Open Science at the MNI
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    CCNA Case Example

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    • Canadian Consortium for Neurodegeration in Aging

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    • Pan Canadian Study

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    • $35 million study

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    • More than 30 sites

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    • Important project for this lab!

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    Automated PET recognition

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    Automated PET recognition

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    Enhanced DICOM anonymization

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    • Going dcmtk free -- PYDICOM
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    • CONDA
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    • Satra knows everything!!
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    Enhanced DICOM anonymization

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    +