Difference between revisions of "Modules:MRIBiasFieldCorrection-Documentation-3.6"
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* Sylvain Jaume: MIT CSAIL | * Sylvain Jaume: MIT CSAIL | ||
* Nicolas Rannou: ISEN IRISA | * Nicolas Rannou: ISEN IRISA | ||
| + | * Nicholas Tustison: UPenn (N3 and N4) | ||
* Ron Kikinis: Harvard Medical School SPL | * Ron Kikinis: Harvard Medical School SPL | ||
* Contact: [http://people.csail.mit.edu/sylvain sylvain at csail.mit.edu] | * Contact: [http://people.csail.mit.edu/sylvain sylvain at csail.mit.edu] | ||
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| − | * '''Step 15/24. :''' | + | * '''Step 15/24. Click on the lower left tab to disable the overlay of the mask image:''' |
** '''Input Image:''' input image | ** '''Input Image:''' input image | ||
** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ||
** '''Output Volume:''' corrected image | ** '''Output Volume:''' corrected image | ||
| − | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_15.png|thumb|280px|Step 15]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_15.png|thumb|280px|Step 15/24 Remove the mask overlay]] |
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{| | {| | ||
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| − | * '''Step 16/24. :''' | + | * '''Step 16/24. Switch to 'None' to remove the overlay. The output image appears in the orthogonal views:''' |
** '''Input Image:''' input image | ** '''Input Image:''' input image | ||
** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ||
** '''Output Volume:''' corrected image | ** '''Output Volume:''' corrected image | ||
| − | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_16.png|thumb|280px|Step 16]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_16.png|thumb|280px|Step 16/24. Switch to 'None']] |
|} | |} | ||
{| | {| | ||
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| − | * '''Step 17/24. :''' | + | * '''Step 17/24. Disable the overlay for the sagittal and coronal views:''' |
** '''Input Image:''' input image | ** '''Input Image:''' input image | ||
** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ||
** '''Output Volume:''' corrected image | ** '''Output Volume:''' corrected image | ||
| − | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_17.png|thumb|280px|Step 17]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_17.png|thumb|280px|Step 17/24. Disable all overlays]] |
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{| | {| | ||
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| − | * '''Step 18/24. :''' | + | * '''Step 18/24. Click on the 'closed eye' icon to display the output image in the 3D rendering window:''' |
** '''Input Image:''' input image | ** '''Input Image:''' input image | ||
** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ||
** '''Output Volume:''' corrected image | ** '''Output Volume:''' corrected image | ||
| − | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_18.png|thumb|280px|Step 18]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_18.png|thumb|280px|Step 18/24. Click on the 'closed eye' icon]] |
|} | |} | ||
{| | {| | ||
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| − | * '''Step 19/24. :''' | + | * '''Step 19/24. Click on the other 2 'closed eye' icons to display the 3 orthogonal slices in the 3D window:''' |
** '''Input Image:''' input image | ** '''Input Image:''' input image | ||
** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ||
** '''Output Volume:''' corrected image | ** '''Output Volume:''' corrected image | ||
| − | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_19.png|thumb|280px|Step 19]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_19.png|thumb|280px|Step 19/24. Click on the other 2 'closed eye' icons]] |
|} | |} | ||
{| | {| | ||
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| − | * '''Step 20/24. :''' | + | * '''Step 20/24. Hold down your mouse in the 3D window and move to rotate and zoom out:''' |
** '''Input Image:''' input image | ** '''Input Image:''' input image | ||
** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ||
** '''Output Volume:''' corrected image | ** '''Output Volume:''' corrected image | ||
| − | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_20.png|thumb|280px|Step 20]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_20.png|thumb|280px|Step 20/24. Hold down and move your mouse in the 3D window]] |
|} | |} | ||
{| | {| | ||
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| − | * '''Step 21/24. :''' | + | * '''Step 21/24. Go to 'File' and 'Save' to save the output volume:''' |
** '''Input Image:''' input image | ** '''Input Image:''' input image | ||
** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ||
** '''Output Volume:''' corrected image | ** '''Output Volume:''' corrected image | ||
| − | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_21.png|thumb|280px|Step 21]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_21.png|thumb|280px|Step 21/24. Click 'File' and then 'Save']] |
|} | |} | ||
{| | {| | ||
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| − | * '''Step 22/24. :''' | + | * '''Step 22/24. Select the files you want to save. By default the XML description and the output volume are selected:''' |
** '''Input Image:''' input image | ** '''Input Image:''' input image | ||
** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ||
** '''Output Volume:''' corrected image | ** '''Output Volume:''' corrected image | ||
| − | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_22.png|thumb|280px|Step 22]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_22.png|thumb|280px|Step 22/24. Select the files you want to save]] |
|} | |} | ||
{| | {| | ||
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| − | * '''Step 23/24. :''' | + | * '''Step 23/24. Click on the output directory to save to a different directory:''' |
** '''Input Image:''' input image | ** '''Input Image:''' input image | ||
** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ||
** '''Output Volume:''' corrected image | ** '''Output Volume:''' corrected image | ||
| − | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_23.png|thumb|280px|Step 23]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_23.png|thumb|280px|Step 23/24. Click on the directory name]] |
|} | |} | ||
{| | {| | ||
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| − | * '''Step 24/24. :''' | + | * '''Step 24/24. For more information, click on the Help tab. The blue link will send you to this page:''' |
** '''Input Image:''' input image | ** '''Input Image:''' input image | ||
** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ** '''Mask Image:''' label map providing an approximative segmentation of the ROI | ||
** '''Output Volume:''' corrected image | ** '''Output Volume:''' corrected image | ||
| − | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_24.png|thumb|280px|Step 24 | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_24.png|thumb|280px|Step 24/24. Click on the Help tab]] |
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Latest revision as of 20:14, 6 May 2010
Home < Modules:MRIBiasFieldCorrection-Documentation-3.6Return to Slicer 3.6 Documentation
Module Name
MRIBiasFieldCorrection
General Information
Module Type & Category
Type: CLI
Category: Filtering
Authors, Collaborators & Contact
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Module Description
MRIBiasFieldCorrection corrects for the intensity inhomogeneity due to MRI gain field distortion. It first estimates the bias field and then 'subtract' it from the image. This module implements the so called methods 'N3' and 'N4' (see references at the bottom of this page).
Usage
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Cheat Sheet
- 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
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:
Doxygen documentation:
More Information
Acknowledgment
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (PI: Ron Kikinis).
References for algorithms implemented in this module
- 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.
- N4ITK: Improved N3 Bias Correction, N.J. Tustison, B.B. Avants, P.A. Cook, Y. Zheng, A. Egan, P.A. Yushkevich, J.C. Gee, IEEE Transactions on Medical Imaging, Vol 99, April 2010.
- N4ITK: Nick's N3 ITK Implementation for MRI Bias Field Correction, N. Tustison, J. Gee, Insight Journal, 2009.
- Parametric Estimate of Intensity Inhomogeneities Applied to MRI, M. Styner, C. Brechbhuler, G. Szekely, and G. Gerig, IEEE Transactions on Medical Imaging, 19(3):153–165, Mar 2000.
