Modules:MRIBiasFieldCorrection-Documentation-3.6

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Gallery of New Features

Module Name

MRIBiasFieldCorrection

User Interface

Output

Caption

General Information

Module Type & Category

Type: CLI

Category: Filtering

Authors, Collaborators & Contact

• Sylvain Jaume: MIT CSAIL
• Nicolas Rannou: ISEN (France)
• Ron Kikinis: BWH Harvard Medical School
• Contact: sylvain at csail.mit.edu

Module Description

The module filters the image to remove the intensity inhomogeneity due to the MRI image acquisition.

Usage

• Load the input dataset (Main menu: Add Volume)
• Create a Mask Volume using the Editor (Modules > Editor) (the Threshold tool should give a good result)
• Select the MRIBiasFieldCorrection module (Modules > Filtering > MRIBiasFieldCorrection)
• In the left panel, select the Input Volume
• Select the Mask Volume
• In the Preview Volume menu , select 'Create New Volume'
• Do the same for the Output Volume menu
• Modify the parameter values if desired (default values gave good results during our experiments)
• Click on Apply.

It took 32 min to process a 512x512x30 MRI volume on a MacBook laptop. To visualize the result:

• Deselect the Overlay volume,
• Select the input as Background volume and the output as Foreground volume.
• Go to Modules > Volumes
• Select the input volume, and write down the values for Window and Level
• Select the output volume, and apply the same values
• Move the lower left cursor in 'Manipulate Slice Views' between B (background) and F (foreground)

Tests

On the Dashboard, these tests verify that the module is working on various platforms:

• MyModuleTest1 MyModuleTest1.cxx
• MyModuleTest2 MyModuleTest2.cxx

Known bugs

Links to known bugs in the Slicer3 bug tracker

• Bug 000: description

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

Links to the module's source code:

Source code:

• Source code

Doxygen documentation:

• class1

More Information

Acknowledgment

This work has been supported by NA-MIC (PI: Ron Kikinis).

References

• A Nonparametric Method for Automatic Correction of Intensity Nonuniformity in MRI Data, J.G. Sled, A.P. Zijdenbos, and A.C. Evans, IEEE Transactions on Medical Imaging, 17(1):87–97, Feb 1998.
• Parametric Estimate of Intensity Inhomogeneities Applied to MRI, M. Styner, C. Brechbhler, G. Szekely, and G. Gerig, IEEE Transactions on Medical Imaging, 19(3):153–165, Mar 2000.
• N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction, Tustison N., Gee J., Insight Journal, 2009.