User tutorial


This tutorial demonstrates features of SlicerIGT that you may use in your own application. You do not need background education in engineering or medicine to follow the tutorials. But it is recommended to get familiar with the basics of 3D Slicer application before starting this course. >> 3D Slicer tutorials

Note that this course will remain under constant development. If you notice any mistakes, or have any suggestions on how to improve it, please contact us.

Sample data

Most tutorials use input from the SlicerIGT-Data folder. Access the folder through >> this link.

You can download the whole SlicerIGT-Data folder as a zip package by clicking on the Download link at the top left of the online data folder.

If a link in the table below is broken, please let us know, and you can always find all presentations in this shared folder:
>> Tutorial presentations

Common topics

Lesson Title Description Prerequisites
U-01 Software installation Install all software that is needed for the rest of this tutorial. Download sample data to work on during the tutorial. None
U-02 Replay recorded data You do not need real hardware devices to try use cases. To replay them on your computer, load saved data in Slicer using the Sequences extension. Or run PLUS in simulation mode. U-01
U-03 Hardware connections Learn how to connect to hardware devices by PLUS, and how to stream data to 3D Slicer for visualization U-01
U-04 Coordinate transformations A practical approach to coordinate systems and transformations U-01
U-05 Command line interface Introduction to the command line user interface. PLUS has many practical functions that are only accessible from this interface. U-01
U-06 Record data with fCal Record live tracker and image data with a small application in PLUS. (No need to run 3D Slicer.) This is useful when you need to record data on a less powerful or 32-bit machine and don't want to run 3D Slicer. U-01
U-07 Record data using Slicer Record live tracker and image data from the convenient GUI of 3D Slicer. U-01
U-08 Hardware prototyping Best practices when building the hardware part of your navigation system. None
U-09 Modeling tools Tools are visualized using 3D model nodes. Some built-in shapes can be used for common tools. Learn visualization options for model nodes. None

Position tracking, navigation

Lesson Title Description Prerequisites
U-11 Pivot calibration How to visualize a tracked pointer device, like a stylus or a needle in Slicer. U-02, U-04, U-09
U-12 Landmark registration Most popular registration method based on two lists of landmarks U-02, U-11
U-13 Surface registration Common registration method based on a list of surface points and a surface model U-12
U-15 Electromagnetic tracking Specific skills and best practices to use electromagnetic position trackers. U-11
U-16 Optical tracking (MicronTracker) Specific skills and best practices to use optical MicronTracker (Claron Technologies) position trackers. U-03
U-17 Optical tracking (Polaris) Specific skills and best practices to use Polaris (NDI) optical position trackers. U-03
U-18 Multi-modality tracking Fusion and synchronization of data streams from two different trackers. U-12
U-19 Distortion field analysis Analyze the accuracy of a less accurate tracker using a more reliable tracker. E.g. check electromagnetic tracking field distortion using an optical tracker. U-12

Intraoperative / real-time imaging

Lesson Title Description Prerequisites
U-31 Tracked ultrasound calibration Compute the position of the ultrasound image relative to the transducer tracker. Synchronize the image and tracking data streams in time. U-01U-02
U-32 Tracked ultrasound visualization in 3D Slicer Show 2D ultrasound in one of Slicer's 2D image viewers. And add tracked ultrasound to the 3D viewers that moves in real time. U-01U-03
U-33 Ultrasound volume reconstruction – offline Convert tracked ultrasound data into a single 3D image that can be handled like CT or MRI data. U-03, U-04
U-34 Ultrasound volume reconstruction – real time See the reconstructed ultrasound in 3D Slicer in real time as you are scanning. U-01U-02
U-37 Brain surgery navigation Build a complete brain surgery navigation system to overview many SlicerIGT functions in one application. U-01U-02

toolkit for navigated interventions