CIVET

The CIVET project was initiated in order to create an environment that allows for easy use of all the important software tools available at the BIC by researchers that are not inclined to delve into the coding and developing of code, as well as offer a flexible platform for developers. The objective is to make it possible for someone with little or no programming background to make full use of the available software for automated structural (anatomical) research, while simultaneously allowing developers to have maximal capacity to customize, add or improve various functions to the platform. I have tried to make available every possible combination of options, and we will soon have a graphical-user interface (GUI) that goes with the scripts that have been developed.

Wiki Synonyms: Civet, civet (Note: this page is not about the species civet)

Version: 1.1.9
***Note that this page is currently undergoing a gradual process of updating.

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Authors

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Project initiated by: Yasser Ad-Dab'bagh
Original versions of the pipeline: Jason Lerch
Early versions of CIVET (pre-modularization): Yasser Ad-Dab'bagh
Current modifications: Claude Lepage
Location: Dr. Alan C. Evans Laboratory (ACE Lab), McConnell Brain-Imaging Centre, Montreal Neurological Institute, McGill University, 3801 University Street, Montreal, Quebec, CANADA, H3A 2B4

The CIVET development project is a team effort. There are currently 6 areas of development

1. Development of a Quarantine-building script: Dale Einarson and Claude Lepage; (See Quarantine-building Development)
2. Maintenance and debugging of quarantine software: Claude Lepage;
3. Initial development and integration of functionality into CIVET: Yasser Ad-Dab'bagh;
4. Modularization of CIVET: Oliver Lyttelton, Sebastian Muehlboeck and Yasser Ad-Dab'bagh;
5. Automated CivetQualityControl components of CIVET: Oliver Lyttelton; and
6. Development of a JAVA-based WIMP-wrapper GUI for CIVET: Yasser Ad-Dab'bagh and Oleg Ivanov (See CIVET-GUI Development).
7. Detailed ongoing documentation (such as this wiki page) by the community of developers working on any component of the project.

Initial documentation (including this wiki page) by: Yasser Ad-Dab'bagh

In addition, invaluable guidance and support was provided by Jason Lerch and Steven Robbins.

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Table of Contents

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1. Basic Introduction
2. Glossary of Terms

3. User's Guide

   • Basic Usage of CIVET

     • Sourcing The Quarantine
     • Preparing Your Data For Processing
     • The CIVET_processing_Pipeline Command Line Interface (CLI)

   • A Summary of Possible Options in CIVET

     • Execution control
     • File options
     • Pipeline options
     • CIVET options
     • VBM options
     • ANIMAL options
     • Pipeline control
     • Stage control
   • The main stages of the CIVET pipeline
   • Common examples of usages
   • Common errors of usage and error messages

4. Developer's Guide

   • Quarantines: Use and Development

   • The PMP Framework

     • What is PMP?
     • What does PMP consist of?
     • How is PMP used?
     • How do I know if a stage was completed?
     • What else does PMP do?
     • Any caveats?
     • Where can I get more information about PMP?
   • The Basic Structure of CIVET
5. Acknowledgments
6. References

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Related Pages

CIVETDev, CIVETVersion, CivetGui, CIVETModules, CIVETDebuggingTool, CivetQualityControl, QuarantineBuildingDev, CivetCheckOut, CivetGuiIdeas, PMP, FullPipeline, Pipeline, CorticalThickness, CLASP, Corticometry, VBC, VBM, N3, INSECT, ANIMAL, SURFREG, SEAL, SGE, PBS, Dr. Alan C. Evans, ACE Lab, YasserAddabbagh, JasonLerch, OliverLyttelton, SebastianMuehlboeck, DaleEinarson, BertVincent, KelvinMok, OlegIvanov, ClaudeLepage, Perl, JAVA, ManualQC

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