For the latest 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.
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.
Most frequently used for these scenarios:
- Use Case 1: Creating a rough brain mask.
- Use Case 2:
Links to tutorials that use this module
Panels and their use
- 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.
- Point to other modules that have similar functionality
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
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