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ANTs tutorial / workshop at the Montreal Neurological Institute

Overview

  • Cooking show format
  • Using data described here

Other questions

  • What image viewer will be used? Should we also install SNAP?

Agenda

May 19

Time Activity
9:00 - 10:00 Introduction, set-up, and ANTs overview (Nick)
10:00 - 10:30 Coffee and questions/discussion
10:30 - 11:30 More ANTs overview (Nick)
11:30 - 12:00 Current research (Brian or Nick)
12:00 - 1:00 Lunch and questions/discussion
1:00 - 2:00 Template preparation for study (Nick)
2:00 - 2:30 Coffee and questions/discussion
2:30 - 3:30 Single subject data prep (Brian)
3:30 - 4:30 Individual/group discussion

May 20

Time Activity
9:00 - 10:00 Review of previous day (Nick)
10:00 - 10:30 Coffee and questions/discussion
10:30 - 11:30 Study setup and execution (Brian)
11:30 - 12:00 Current research (Brian or Nick)
12:00 - 1:00 Lunch and questions/discussion
1:00 - 2:00 Study statistics & visualization I
2:00 - 2:30 Coffee and questions/discussion
2:30 - 3:30 Study statistics & visualization II
3:30 - 4:30 Individual/group discussion

Agenda details

  • Topics
  • questions to be addresed
  • time-specific notes

May 19, 9:00 - 10:00 Introduction and set-up

Topics

* ANTs history & philosophy
    * ANTs origins in SyN
    * collaborators
    * open source and reproducibility
    * competition history
* Development and interface with the user community
    * ITK
    * Github
    * sourceforge and github help forum
    * documentation
* ANTs command line
* Dependencies
    * CMake
    * ITK
    * VTK
* Core programs
    * antsRegistration
    * Atropos
    * N4/N3*
    * KK
    * ImageMath
    * antsSurf
    * antsAI
* Core scripts
    * antsRegistrationSyN(Quick).sh
    * antsBrainExtraction.sh
    * antsAtroposN4.sh
    * antsCorticalThickness.sh
    * antsLongitudinalCorticalThickness.sh
    * buildtemplateparallel.sh/antsMultivariateTemplateConstruction.sh
    * antsMalfLabeling.sh

Questions to be addressed

* What is the history of ANTs/ANTsR?
* Where can I download ANTs/ANTsR?
* How do I install ANTs/ANTsR on my machine?
* Who are the ANTs/ANTsR developers and contributors?
* Where can I get help for problems with ANTs/ANTsR?
* Can I contribute to ANTs/ANTsR?
* How is ITK related to ANTs?
* Where can I find ANTs documentation?
* What is ANTSPATH?
* What does ANTs not do?  (Motivate the use of ANTsR)

Possible interactive activities

* Explore ANTs directory structure
* Explore ANTs sourceforge/Github forum
* Look at ITK doxygen
* Update the ANTs and ANTsR repository
* Set up ANTSPATH
* Run r16/r85 registration

May 19, 10:00 - 10:30 Coffee and questions/discussion

May 19, 10:30 - 11:30 Study data and ANTsR overview

Topics

* Data
    * Nature paper
    * figshare
    * data modifications for tutorial
* ANTsR overview

Questions to be addressed

Possible interactive activities

May 19, 1:00 - 2:00 Template data preparation for study

Topics

* template building
* mapping other modalities

Questions to be addressed

Possible interactive activities

* Create a T1-weighted template
* Create a multivariate template
* Create a symmetric template
* Create priors for the template
* Create cortical labels for the template

May 19, 2:30 - 3:30 Single subject data preparation for study

Topics

* template building
* mapping other modalities through the T1

Questions to be addressed

Possible interactive activities

* Create a T1-weighted template
* Create a multivariate template
* Create a symmetric template
* Create priors for the template
* Create cortical labels for the template

May 20, 9:00 - 10:00 Review of previous day

Topics

  • XX

Questions to be addressed

Possible interactive activities