MRI Bias Field Correction
This module enables the user to get a fast preview of the Bias Field Correction applied on a 2D slice. The advantage of this preview is to try different parameters and visualize the effect in real time.
A Command Line version of this module has been developed to enable the Slicer3 Testing framework. Hence this module is tested during every Nightly build and the result is reported in the Slicer3 Dashboard.
Module Type & Category
Type: Interactive or CLI
Authors, Collaborators & Contact
- Nicolas Rannou: Harvard Medical School, Brigham and Women's Hospital
- Sylvain Jaume: MIT Computer Science and Artificial Intelligence Laboratory
- Contact: <nrannou at bwh.harvard.edu>, <sylvain at csail.mit.edu>
The module filters the image to remove the intensity inhomogeneity due to the MRI image acquisition.
- 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)
Examples, Use Cases & Tutorials
- Note use cases for which this module is especially appropriate, and/or link to examples. (to be defined)
- Link to examples of the module's use (to be defined)
- Link to any existing tutorials (to be defined)
Quick Tour of Features and Use
List all the panels in your interface, their features, what they mean, and how to use them. For instance:
- Input panel:
- Parameters panel:
- Output panel:
- Viewing panel:
No other modules or packages are required to use this module.
Follow this link to the Slicer3 bug tracker.
Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.
Source code & documentation
This work has been supported by NA-MIC Algorithms.
- 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.