Documentation/Nightly/Extensions/MatlabBridge

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Introduction and Acknowledgements

Author: Andras Lasso (PerkLab, Queen's University), Jean-Christophe Fillion-Robin (Kitware), Kevin Wang (Radiation Medicine Program, Princess Margaret Hospital, University Health Network Toronto)
Contact: Junichi Tokuda <email> tokuda@bwh.harvard.edu</email>
Contact: Andras Lasso, <email>lasso@cs.queensu.ca</email>
Website: http://www.slicerrt.org
License: Slicer license

SparKit   NA-MIC

Extension Description

MatlabBridge is an extension of 3D Slicer to allow running Matlab functions directly in 3D Slicer as a command-line interface (CLI) module. Running Matlab functions does not require any extra programming, only the creation of a simple XML file that describes the inputs and outputs of the Matlab function. No building or installation of any additional components are needed - only Slicer and Matlab has to be installed on the computer.

Modules

• Matlab Module Generator
• Matlab Commander

Use Cases

• 

  Example Matlab module user interface in Slicer

• 

  Matlab Bridge modules appear under the Developer Tools / Matlab category

• 

  A skeleton Matlab script can be created and installed using the Matlab module generator.

• 

  The Matlab Commander allows running any commands from the user interface or from another Slicer module.

See also this demo video.

Tutorials

Example: Implementing a simple image thresholding and statistics module in Matlab

• Install the MatlabBridge extension
• Open the Developer Tools / Matlab / Matlab Module Generator module
• Specify the path to your Matlab.exe (such as c:\Program Files\MATLAB\R2012a\bin\matlab.exe)
• Enter your module name, such as MyThresholder and click Generate module. Take note of the file paths shown in the status window.
• Edit your MyThresholder.m file to implement the algorithm and computations. Example:

function outputParams=MatlabModuleTemplate(inputParams)

img=cli_imageread(inputParams.unnamed{1});

outputParams.min=min(min(min(img.pixelData)));
outputParams.max=max(max(max(img.pixelData)));

img.pixelData=(double(img.pixelData)>inputParams.threshold)*100;

cli_imagewrite(inputParams.unnamed{2}, img); 

• Edit the generated skeleton MyThresholder.xml file that describes your algorithm inputs and outputs. Slicer will automatically generate the graphical user interface to be able to specify the inputs and display the outputs. Example:

<?xml version="1.0" encoding="utf-8"?>
<executable>
  <category>Matlab</category>
  <title>MyThresholder</title>
  <description><![CDATA[Perform a simple image processing and image statistics computation in Matlab.]]></description>
  <version>0.0.0.1</version>
  <documentation-url>http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT</documentation-url>
  <license/>
  <contributor>Andras Lasso (PerkLab)</contributor>
  <acknowledgements><![CDATA[SparKit is a project funded by Cancer Care Ontarioand the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) to provide free, open-source toolset for radiotherapy and related image-guided interventions.]]></acknowledgements>
  <parameters>
    <label>Processing Parameters</label>
    <description><![CDATA[Parameters for the processing]]></description>
    <integer>
      <name>threshold</name>
      <longflag>--threshold</longflag>
      <description><![CDATA[All voxels below this value will be set to zero]]></description>
      <label>Threshold</label>
      <default>50</default>
      <constraints>
        <minimum>-2000</minimum>
        <maximum>5000</maximum>
        <step>5</step>
      </constraints>      
    </integer>
  </parameters>
  <parameters>
    <label>IO</label>
    <description><![CDATA[Input/output parameters]]></description>
    <image>
      <name>inputVolume</name>
      <label>Input Volume</label>
      <channel>input</channel>
      <index>0</index>
      <description><![CDATA[Input volume to be filtered]]></description>
    </image>
    <image>
      <name>outputVolume</name>
      <label>Output Volume</label>
      <channel>output</channel>
      <index>1</index>
      <description><![CDATA[Output filtered]]></description>
    </image>
  </parameters>
  <parameters>
    <label>Output</label>
    <description>Matlab command output</description>
    <double>
      <name>min</name>
      <label>Minimum</label>
      <channel>output</channel>
      <default></default>
      <description><![CDATA[Image mininum]]></description>
    </double>    
    <double>
      <name>max</name>
      <label>Maximum</label>
      <channel>output</channel>
      <default></default>
      <description><![CDATA[Image maximum]]></description>
    </double>    
  </parameters>
</executable>

• Restart Slicer
• Download the MRIHead image sample using the Download Sample Data module
• Open the Matlab / MyThresholder module
• Select the MRIHead image as input, create a new volume as output, click Apply
• Click AutoRun at the bottom of the module user interface then change the threshold value with the slider, the processed image will be updated automatically

References

• Overview of issues and enhancement requests

Information for Developers

See some information on the design of the module at the 2013 Summer Project week wiki.