Difference between revisions of "Documentation/4.0/Modules/N4ITKBiasFieldCorrection"

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This module is especially appropriate for these use cases:
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* Image acquisition is done with a surface coil, and you observe signal fall-off as you get further away from the coil (this is particularly the case at higher field strengths)
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* You observe smooth variation of the intensity over the tissue that should have intensity close to uniform
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* Your attempts to segment or register your data are not successful, and you are not sure what to do next
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Examples of the module in use:
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* Correction of the signal inhomogeneity in prostate MRI obtained with endorectal coil at 3T field strength
 
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* Correction of the bias in vervet MRI. Acquisition parameters: 3T GE scanner, single-channel dedicated RF coil (Litzcage, Doty Scientific, Columbia, SC); 3D SPGR sequence (TI 600ms, TE 3.276ms, TR 15.28ms; flip angle 15 deg; matrix 256x256; FOV 12cm; in-plane resolution 0.47 mm; slice thickness 0.5 mm).
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|[[Image:n4_mark1_input.png|thumb|280px|Slice of the input test volume with apparent bias field and label outlines]]
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Most frequently used for these scenarios:
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|[[Image:n4_mark1_output.png|thumb|280px|Output image visually contains less inhomogeneity]]
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* Use Case 1: Preprocessing to compensate for inhomogeneous coil reception profile in MR images
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|[[Image:n4_mark1_subtract.png|thumb|280px|Before - After subtract image]]
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** before segmenting an inherently homogeneous structure
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** before registration
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Revision as of 13:58, 20 October 2011

Home < Documentation < 4.0 < Modules < N4ITKBiasFieldCorrection


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. The development of this module was supported in part by NIH grants R01 AA016748-01, R01 CA111288 .... check grants.
  • Authors: Nick Tustison (N4ITK filters), Ron Kikinis (PI + design and inspiration), Andrey Fedorov (design, ITK filter modifications, 3D Slicer module)
  • Contact: Andrey Fedorov, <email>fedorov@bwh.harvard.edu</email>
Template:Documentation/4.0/module-introduction-logoTemplate:Documentation/4.0/module-introduction-logo

Module Description

Template:Documentation/4.0/module-cli-description

Use Cases

This module is especially appropriate for these use cases:

  • Image acquisition is done with a surface coil, and you observe signal fall-off as you get further away from the coil (this is particularly the case at higher field strengths)
  • You observe smooth variation of the intensity over the tissue that should have intensity close to uniform
  • Your attempts to segment or register your data are not successful, and you are not sure what to do next

Examples of the module in use:

  • Correction of the signal inhomogeneity in prostate MRI obtained with endorectal coil at 3T field strength
Prostate erMRI
After bias correction
Before - After subtract image
Recovered bias field
  • Correction of the bias in vervet MRI. Acquisition parameters: 3T GE scanner, single-channel dedicated RF coil (Litzcage, Doty Scientific, Columbia, SC); 3D SPGR sequence (TI 600ms, TE 3.276ms, TR 15.28ms; flip angle 15 deg; matrix 256x256; FOV 12cm; in-plane resolution 0.47 mm; slice thickness 0.5 mm).
Slice of the input test volume with apparent bias field and label outlines
Output image visually contains less inhomogeneity
Before - After subtract image
Recovered bias field


Tutorials

Links to tutorials that use this module

Panels

Template:Documentation/4.0/module-cli-parametersdescription

Panels

  • 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

Work in progress
 Section under construction.


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