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Information Systems Program

ITK-SNAP Training 05252010

ITK-SNAP Training Course at NCI-Frederick

Paul A. Yushkevich, Ph.D.
Assistant Professor of Radiology, University of Pennsylvania
NCI-Frederick, Bldg 549, Library Training Room
Date: Tuesday, May 25th, 2010
Time slots: 10AM – 1PM and 2PM – 5 PM

Course Overview

ITK-SNAP is a software tool for viewing and labeling 3D medical images. This three-hour course will introduce students to the tool through hands on exercises and instructor-led demos. By the end of the course, attendees will be able to use basic and advanced features of ITK-SNAP.


Only basic computer skills are required.

Course Outline

The course is organized into seven modules. Modules 2-6 include a theoretical component, an instructor-led live demo, and an exercise for the attendees. All data for the exercises will be provided.

1. Introduction
2. Using ITK-SNAP as an image viewer
3. Manual segmentation
4. Automatic segmentation
5. Multiple ITK-SNAP sessions and layers
6. Advanced topics

Course Objectives

The objectives for each course module are listed below. They describe the set of tasks that attendees should be able to perform after completing the module.

Module 1. Introduction

Explain where to find help for ITK-SNAP

  • Open the help browser from the ITK-SNAP menu
  • View and post to the itksnap-users mailing list

Module 2. Using ITK-SNAP as an image viewer

  • Open structural NIfTI and DICOM format images in ITK-SNAP using the GUI
  • Perform basic image navigation commands
    • Move cursor in three dimensions using the mouse and keyboard
    • Change zoom level using mouse motion and exact zoom level specification
    • Pan using mouse motion and thumbnail interface
  • Adjust image contrast
    • Using level and window controls
    • Using the curve control
    • Automatically
    • Demonstrate different ways to view the image histogram
  • Obtain information about the image
    • Explain all fields displayed in the Image Info dialog
    • Specify exact cursor coordinates
    • Explain the relationship between the image space and the physical space
    • Correct or change image orientation using the GUI

Module 3. Manual Segmentation

  • Perform manual segmentation using the polygon tool
    • Describe how the segmentation is represented in ITK-SNAP
    • Describe how the active and draw-over label affect drawing operations
    • Draw closed polygons
    • Edit polygons by inserting, deleting and moving vertices
    • Modify and add segmentation labels using the segmentation label editor
    • Change the opacity of individual labels and the whole segmentation
    • Undo and redo changes to the segmentation
    • Render segmentation as a 3D mesh
    • Save segmentation results to a file
  • Perform manual segmentation using the paintbrush tool
    • Switch between foreground and background labels using mouse buttons
    • Change the size and shape of the paintbrush
    • Perform semi-automatic segmentation using the adaptive brush
    • Describe the differences in behavior of 2D and 3D brush shapes

Module 4. Automatic Segmentation

  • Give an intuitive explanation of active contour method
  • Define the concept of speed function
  • Describe the differences, relative advantages, and limitations of edge-based and intensity-based active contour segmentation approaches and match these approaches to real-world
  • segmentation problems.
  • Automatically segment the ventricles in a brain MRI image using both approaches
  • Illustrate how the topology of the segmentation can change during active contour evolution
  • Describe how to speed up segmentation in ITK-SNAP using sub-sampling, time step changes.

Module 5. Multiple ITK-SNAP Sessions and Layers

  • Open multiple image layers in ITK-SNAP
    • Describe distinction between main, overlay, and segmentation image layers.
    • Describe how ITK-SNAP handles floating point images
    • Describe how ITK-SNAP handles color (RGB) images
    • Load and unload scalar and RGB image overlays
    • Change appearance of scalar image overlays using contrast and color map controls
  • Use multiple ITK-SNAP sessions at once
    • Describe how the cursors between ITK-SNAP sessions are linked
    • Concurrently view multi-modality images of the same subject in two ITK-SNAP sessions
    • Turn multi-session features on and off
    • Manage screen space by changing the dimensions of ITK-SNAP interface

Module 6. Advanced Topics

  • Generate figures and data for publication using ITK-SNAP
    • Change the appearance of display elements in the GUI
    • Show and hide display elements using the keyboard
    • Take screenshots and screenshot series
    • Save information on volumes and statistics
  • Perform advanced image processing operations with Convert3D, a companion tool to ITK-SNAP
    • Change header information from image to image
    • Split a segmentation into individual labels
    • Correct inhomogeneity bias in an MRI image
    • Post-process segmentation results using dilation, erosion, and connected components operations.