Documentation/Nightly/Modules/LineMarkerRegistration

Introduction and Acknowledgements

This work is part of the National Center for Image Guided Therapy (NCIGT) (P41 EB015898), National Alliance for Medical Image Computing (NA-MIC) (U54 EB005149), and other research grants (R01 CA111288, R01 CA138586) funded by National Institutes of Health and CIMIT. Author: Junichi Tokuda, BWH Contact: Junichi Tokuda, <email>tokuda@bwh.harvard.edu</email>

Surgical Planning Laboratory (SPL)

Module Description

The Line Marker Registration CLI automatically detects a fiducial marker consisting of multiple lines on a 3D image and register the marker to the image coordinate system. The users can configure the CLI to use their own fiducial marker design by creating a marker configuration file formatted in CSV.

Use Cases

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Tutorials

Installation

Currently this CLI is not available in Slicer Extension. Please obtain the source code from Git repository and build it by following the instruction.

Example Data

Example fiducial marker data (MR-visible z-frame) comes with the source code. There are three files in the "Examples" directory:

• zframe-config.csv (Example fiducial marker configuration file)
• zframe-image.nrrd (MR image of example fiducial marker)
• zframe-model.vtk (VTK model of fiducial marker)

Step by step instruction

First, load the MR image and the VTK model to the Scene.

You will see the model and the image in the 2D/3D viewer.

From the Modules menu, go to "IGT" > "LineMarkerRegistration. The panel of the CLI looks:

Select input volume, marker configuration file, output volume (where the result of marker segmentation is stored) and marker transform from IO menu as follows:

• Input Volume: "zframe-image"
• Marker Config File: Click the button next to the text input, and choose "zframe-config.csv" which is in the Examples folder in the source.
• Output Volume: Choose "Create new Volume" to create a new scalar volume node.
• Marker Volume: Choose "Create new LinearTransform" to create a new linear transform node.

Leave other parameters the default value (the values are adjusted for the example data). Now you can click the "Apply" button to run the CLI. It usually takes 2-10 seconds to complete. If it is successful, you could see the segmented line markers on the 2D viewers:

Panels and their use

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Similar Modules

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References

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