UVa Tutorial

UVa Tutorial (May 15-16, 2017)

Agenda

Day 1 morning: ANTs intro, registration, and template building

• Intro (slideshow)
  • history of ANTs
  • ITK
  • developers
• Logistics
  • github
  • sourceforge
  • How does one ask questions, report bugs?
• dcm2niix
• public data (NKI, IXI, etc. templates) on figshare
• ITK SNAP (loading image data), discussion of image formats
• finish set-up for people who haven’t installed everything
• command line discussion
  • --help 1, -h 1
  • "functional notation"
• registration and template building
  • What is the appeal of ANTs? (won competitions, based on ITK)
  • Difference between antsRegistration.cxx and ANTS.cxx
  • ANTs registration
    • antsRegistrationSyN.sh, antsRegistrationSyNQuick.sh
    • example: https://github.com/ntustison/ProtonCtLungMaskRegistration
    • example: download TemplateBuildingExample and use BrainSlices
      • show difference in ants…SyN.sh and ants…SyNQuick.sh
      • show multi-modal use, i.e. ants…SyN.sh -d 3 .. -f image1a -f image1b -m image2a -m image2b
    • example: https://github.com/ntustison/antsCtLungRegistrationExample
    • example Large deformation: https://github.com/stnava/C
  • Template building
    • differences between buildtemplateparallel.sh, antsMultivariateTemplateConstruction.sh, and antsMultivariateTemplateConstruction2.sh
    • example: https://github.com/ntustison/CongressionalFaceTemplates
    • example Template: https://github.com/ntustison/TemplateBuildingExample
    • example SST: https://github.com/ntustison/SingleSubjectTemplateExample
  • discuss antsAI (NEED EXAMPLE: modify chicken to use antsAI)

Day 1 afternoon: ANTs preprocessing, useful scripts, visualization

• preprocessing
  • example Denoising: https://github.com/ntustison/DenoiseImageExample
  • example Denoising: try on 2-D slice from CT registration example above DenoiseImage -d 2 -i testRescaled.nii.gz -o test2.nii.gz -v 1 -p 2x2 -r 4x4
  • example N3BiasFieldCorrection, N4BiasFieldCorrection
    • Brian likes to use N3 for fMRI preprocessing (not as aggressive)
    • Run N4 on the image from the Denoising example
• segmentation
  • Atropos (use antsAtroposN4 examples)
    • brain, example: https://github.com/ntustison/antsAtroposN4Example
    • lung, example: https://github.com/ntustison/LungVentilationSegmentationExample
  • joint label fusion
    • brain, example: https://github.com/ntustison/MalfLabelingExample
    • lung, example: https://github.com/ntustison/LungAndLobeEstimationExample
    • jif, example: https://github.com/ntustison/JointIntensityFusionExample
• Useful scripts
  • example: https://github.com/ntustison/antsVisualizationExamples
  • antsBrainExtraction.sh, example: https://github.com/ntustison/antsBrainExtractionExample
  • antsCorticalThickness.sh/antsLongitudinalCorticalThickness.sh, example: https://github.com/ntustison/antsCorticalThicknessExample
  • antsJointLabelFusion.sh
• Visualization
  • example: https://github.com/ntustison/antsVisualizationExamples
  • discuss Paraview

Day 2 morning: ANTsR basics

• Why integrate with ANTs with R?
• read/write images
• plot
• ANTs commands in ANTsR: (NEED TO PRACTICE THIS PART)
  • antsRegistration
  • n4BiasFieldCorrection, n3BiasFieldCorrection

Day 2 afternoon: ANTsR advanced

• fMRI processing
  • tutorial: https://github.com/ntustison/ANTsRfMRITutorial
• SCCAN tutorial
  • tutorial: https://github.com/ntustison/BrianSccanTutorial