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ANTs tutorial / workshop at MD Anderson: Aug 11-12, 2016

Overview

  • Discussion and demonstration format:
    • We would like to promote as much interaction as possible.
    • The content can easily be adapted "on the fly" depending on audience interest and participation.
  • Using data described here
  • Supplemented with a couple of elderly subject datasets.

Software

The above tools depend on R and cmake.

Supported platforms include OSX and Linux variants. These may work on windows but no promises.

Visualization

Datasets

Agenda

August 11

Day 1: The ANTs framework for adaptable registration and segmentation

Time Activity Presenter Notes
9:00 - 9:15 Setup NT --
9:15 - 10:00 Overview of 2014 Nimg paper NT see associated paper
10:00 - 10:30 Coffee and questions/discussion -- --
10:30 - 12:00 ANTs Registration BA define transforms, metrics, connect to cars, C, chicken
12:00 - 1:00 Lunch and questions/discussion -- --
1:00 - 2:00 Template building and mapping multiple modalities (MMM) NT github examples, antsmultimodality, and applying transforms to other modalities (maybe use PTBP full MM subject as example or the petSUVR example below)
2:00 - 2:30 Coffee and questions/discussion -- --
2:30 - 3:00 PTBP and Joint Label Fusion / building priors BA Joint Label Fusion (JLF)
3:00 - 3:30 ANTs Segmentation: Atropos, 2nd JLF example, Multi-Resolution Voxelwise Neighborhood Random Forest (MRVNRF)/rfLesionSeg BA + NT setup research talk (if needed), perhaps use PTBP_Intro
3:30 - 4:00 Research topics and/or discussion NT continue segmentation discussion here: stroke, tumor, WMH?

August 12

Day 2: The ANTsR framework for multivariate statistics and prediction

Time Activity Presenter Notes
9:00 - 10:00 Review of previous day, address questions, intro ANTsR NT + BA modify as needed
10:00 - 10:30 Coffee and questions/discussion -- --
10:30 - 11:00 Visualization of surfaces or volumes NT antsSurf, antsVol, CreateTiledMosaic, plot.antsImage
11:00 - 12:00 Let's perform a "real study" BA PTBP and VBM results
12:00 - 1:00 Lunch and questions/discussion -- --
1:00 - 2:00 Functional MRI or Dimensionality reduction in ANTsR BA Eigenanatomy - could do ICA/blindsource
2:00 - 2:30 Coffee and questions/discussion -- --
2:30 - 3:00 Prediction & visualization NT BrainAge ... Multiple modality age/cog prediction in PTBP
3:00 - 4:00 Individual/group discussion NT + BA review, prepare for after party?

Backup topics

TODO

  • BA: antsRegistration (should be fun): generality (species, organs), priors, framework, command line

  • BA: rsf examples (briefly: alff, correlations, motion, nuisance) + get data!

  • BA: test ASL example and add data

  • BA: dimRed examples (use basic presentation, then follow with ANTsR examples, take some content from RMI)

  • BA: brainAge implementation across modalities with and without sparseness

  • BA: process the MMM subject in ANTsR

August 11: The ANTs framework for adaptable registration and segmentation

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/antsVol
    * antsAI
    * antsJointFusion
* Core scripts
    * antsRegistrationSyN(Quick).sh
    * antsBrainExtraction.sh
    * antsAtroposN4.sh
    * antsCorticalThickness.sh
    * buildtemplateparallel.sh/antsMultivariateTemplateConstruction.sh
    * antsJointLabelFusion.sh
* Data
    * Nature paper
    * figshare
    * data modifications for tutorial
* ANTsR overview
* template building
* mapping other modalities
* template building
* mapping other modalities through the T1

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
* Create a T1-weighted template
* Create a multivariate template
* Create a symmetric template
* Create priors for the template
* Create cortical labels for the template
* Apply priors to new data

August 12: Multivariate statistics, visualization and prediction

Topics

  • We will first refresh topics from day one and cover material that we missed.

  • We will also refine day 2 material given the feedback from day 1.

  • Statistical analyses with ANTs and ANTsR

Questions to be addressed

  • How do I compute population statistics with ANTs data?

  • How do I visualize statistical results?

  • How do I perform predictive studies? E.g. compute brainAge?

Possible interactive activities

  • See: ANTsTutorial for an overview of material.

    • ANTsR VBM

    • ANTsR brainAge

    • ANTsR dimensionality reduction

  • See the examples here.