Difference between revisions of "Modules:MRIBiasFieldCorrection-Documentation-3.6"
From Slicer Wiki
Sylvainjaume (talk | contribs) |
Sylvainjaume (talk | contribs) (→Usage) |
||
| Line 39: | Line 39: | ||
{| | {| | ||
| | | | ||
| − | * '''Step 1/24. | + | * '''Step 1/24. To open the input image, click on 'File' and then 'Add 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_01.png|thumb|280px|Step 1]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_01.png|thumb|280px|Step 1/24. Add the input volumes]] |
|} | |} | ||
{| | {| | ||
| | | | ||
| − | * '''Step 2/24. Select | + | * '''Step 2/24. Select the input image and click Apply:''' |
** '''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_02.png|thumb|280px|Step 2]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_02.png|thumb|280px|Step 2/24. Select the input image]] |
|} | |} | ||
{| | {| | ||
| | | | ||
| − | * '''Step 3/24. :''' | + | * '''Step 3/24. The input image appears in the axial-sagittal-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_03.png|thumb|280px|Step 3]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_03.png|thumb|280px|Step 3/24. Image displayed in the orthogonal views]] |
|} | |} | ||
{| | {| | ||
| | | | ||
| − | * '''Step 4/24. :''' | + | * '''Step 4/24. Select the mask image. Check the box 'Label Map' and click Apply:''' |
** '''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_04.png|thumb|280px|Step 4]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_04.png|thumb|280px|Step 4/24. Select the mask image as a label map]] |
|} | |} | ||
{| | {| | ||
| | | | ||
| − | * '''Step 5/24. :''' | + | * '''Step 5/24. The label map is overlaid on the axial-sagittal-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_05.png|thumb|280px|Step 5]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_05.png|thumb|280px|Step 5/24. Label map overlaid on the input image]] |
|} | |} | ||
{| | {| | ||
| | | | ||
| − | * '''Step 6/24. :''' | + | * '''Step 6/24. Click on Modules and scroll-down the menu:''' |
** '''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_06.png|thumb|280px|Step 6]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_06.png|thumb|280px|Step 6/24. List of Slicer 3.6 modules]] |
|} | |} | ||
{| | {| | ||
| | | | ||
| − | * '''Step 7/24. :''' | + | * '''Step 7/24. Select 'Filtering' and then 'MRIBiasFieldCorrection':''' |
** '''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_07.png|thumb|280px|Step 7]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_07.png|thumb|280px|Step 7/24. Select MRIBiasFieldCorrection in Filtering]] |
|} | |} | ||
{| | {| | ||
| | | | ||
| − | * '''Step 8/24. :''' | + | * '''Step 8/24. The User Interface of MRIBiasFieldCorrection appears:''' |
** '''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_08.png|thumb|280px|Step 8]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_08.png|thumb|280px|Step 8/24. User interface of MRIBiasFieldCorrection]] |
|} | |} | ||
{| | {| | ||
| | | | ||
| − | * '''Step 9/24. :''' | + | * '''Step 9/24. Select the input image in the list of loaded volumes:''' |
** '''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_09.png|thumb|280px|Step 9]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_09.png|thumb|280px|Step 9/24. Select input among loaded volumes]] |
|} | |} | ||
{| | {| | ||
| | | | ||
| − | * '''Step 10/24. :''' | + | * '''Step 10/24. Select the mask image in the list of loaded volumes:''' |
** '''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_10.png|thumb|280px|Step 10]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_10.png|thumb|280px|Step 10/24. Select mask among the loaded label maps]] |
|} | |} | ||
{| | {| | ||
| | | | ||
| − | * '''Step 11/24. :''' | + | * '''Step 11/24. Create a new node for the output in Slicer MRML tree:''' |
** '''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_11.png|thumb|280px|Step 11]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_11.png|thumb|280px|Step 11/24. Create node in MRML tree for output]] |
|} | |} | ||
{| | {| | ||
| | | | ||
| − | * '''Step 12/24. :''' | + | * '''Step 12/24. Click 'Apply' to run the N3 algorithm (default):''' |
** '''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_12.png|thumb|280px|Step 12]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_12.png|thumb|280px|Step 12/24. Run the N3 algorithm]] |
|} | |} | ||
{| | {| | ||
| | | | ||
| − | * '''Step 13/24. :''' | + | * '''Step 13/24. 'Status Running' means the algorithm is running. Note 'Running...' in lower bar:''' |
** '''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_13.png|thumb|280px|Step 13]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_13.png|thumb|280px|Step 13/24. Status info when algorithm is running]] |
|} | |} | ||
{| | {| | ||
| | | | ||
| − | * '''Step 14/24. :''' | + | * '''Step 14/24. 'Status Completed' means the algorithm is done. Note 'Completed' in lower bar:''' |
** '''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_14.png|thumb|280px|Step 14]] | + | |[[Image:MRIBiasFieldCorrection_Slicer3.6_Documentation_14.png|thumb|280px|Step 14/24. Status info when algorithm is done]] |
|} | |} | ||
Revision as of 04:59, 2 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
|
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
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 Screenshot of the MRIBiasFieldCorrection module in Slicer3 during development. The screenshot illustrates the application of the MRI Bias Field Correction on the SPL Atlas. Note that the interface was simplified for the production version. The top left window shows the mask used to defined the ROI where the correction will be applied. The top right window shows the rendering of the 3D model created using the mask. The bottom left window shows one slice in the input image. Note the intensity inhomogeneity from the bottom left corner (dark) to the top right corner (bright). The bottom right window shows the output image after the application of the MRI Bias Field Correction module. The parameters used for the correction are shown on the left panel of the Slicer3 interface. |
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.
