Documentation/Nightly/Modules/ForegroundMasking

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For the stable Slicer documentation, visit the 4.10 page.

Introduction and Acknowledgements

This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the NA-MIC website.
Author: Hans Johnson, UIOWA
Contact: Hans Johnson,

University of Iowa  
Surgical Planning Laboratory  

Module Description

This program is used to create a mask over the most prominant forground region in an image. This is accomplished via a combination of otsu thresholding and a closing operation. More documentation is available here: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ForegroundMasking.


Use Cases

Most frequently used for these scenarios:

  • Use Case 1: Creating a rough brain mask.
  • Use Case 2:

Tutorials

Links to tutorials that use this module

Panels and their use

Parameters:

  • IO: Input/output parameters
    • Input Image Volume (inputVolume): The input image for finding the largest region filled mask.
    • Output Mask (outputROIMaskVolume): The ROI automatically found from the input image.
    • Output Image (outputVolume): The inputVolume with optional [maskOutput|cropOutput] to the region of the brain mask.
    • Mask Output (maskOutput): The inputVolume multiplied by the ROI mask.
    • Output Image Clipped by ROI (cropOutput): The inputVolume cropped to the region of the ROI mask.
  • Configuration Parameters:
    • Otsu Percentile Threshold (otsuPercentileThreshold): Parameter to the Otsu threshold algorithm.
    • Otsu Correction Factor (thresholdCorrectionFactor): A factor to scale the Otsu algorithm's result threshold, in case clipping mangles the image.
    • Closing Size (closingSize): The Closing Size (in millimeters) for largest connected filled mask. This value is divided by image spacing and rounded to the next largest voxel number.
    • ROIAuto Dilate Size (ROIAutoDilateSize): This flag is only relavent when using ROIAUTO mode for initializing masks. It defines the final dilation size to capture a bit of background outside the tissue region. At setting of 10mm has been shown to help regularize a BSpline registration type so that there is some background constraints to match the edges of the head better.
    • Output Image Pixel Type (outputVolumePixelType): The output image Pixel Type is the scalar datatype for representation of the Output Volume.
    • Number Of Threads (numberOfThreads): Explicitly specify the maximum number of threads to use.


List of parameters generated transforming this XML file using this XSL file. To update the URL of the XML file, edit this page.


Similar Modules

  • Point to other modules that have similar functionality

References

Publications related to this module go here. Links to pdfs would be useful. For extensions: link to the source code repository and additional documentation

Information for Developers