From SlicerWiki

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: Sylvain Jaume, MIT CSAIL Contributor1: Nicolas Rannou, ISEN IRISA Contributor2: Nicholas Tustison, UPenn Contributor3: Ron Kikinis, SPL Contact: Sylvain Jaume,

MIT CSAIL   Surgical Planning Laboratory

Module Description

Corrects 3D MRI images corrupted by MRI gain field effect. This module removes the slow-varying intensity variation from a 3D image. The output image has a higher contrast locally and the visualization and reading of the image are improved. This is an important pre-processinbg step for image operations requiring intensity perfect images, such as the Expectation Maximization segmentation (see EMSegment module). The N3 and N4 methods are described in N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction, Tustison N., Gee J., Insight Journal, 2009. http://hdl.handle.net/10380/3053 The Slicer code was contributed by Sylvain Jaume (MIT) for NA-MIC (http://na-mic.org).

Use Cases

Most frequently used for these scenarios:

• Use Case 1:

MRIBiasFieldCorrection corrects for the intensity inhomogeneity in 3D MRI images. Left image: input image with intensity inhomogeneity from lower corner to higher corner. Right image: output image where the intensity inhomogeneity has been corrected.

Tutorials

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Panels

Parameters:

• IO
  • Input Image: Input image
  • Input Mask: Input mask
  • Output Image: Corrected image
• Parameters for the algorithm
  • Algorithm type: Select your algorithm
  • Shrink factor: Shrink the image by this factor
  • Maximum number of iterations: Number of iterations
  • Number of fitting levels: Set the number of fitting levels
  • Wiener filter noise: Set the Wiener filter noise
  • Bias full width at half maximum: Set the bias field full width at half maximum
  • Convergence threshold: Set the convergence threshold

Similar Modules

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References

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Information for Developers

Section under construction.