Modules:MRIBiasFieldCorrection-Documentation-3.6 - Revision history

Sylvainjaume: /* Authors, Collaborators & Contact */

2010-05-06T20:14:08Z

Authors, Collaborators & Contact

Sylvainjaume: /* Usage */

2010-05-02T05:32:41Z

Usage

Sylvainjaume: /* Module Name */

2010-05-02T05:04:12Z

Module Name

Sylvainjaume: /* Module Name */

2010-05-02T05:02:53Z

Module Name

Sylvainjaume: /* Module Name */

2010-05-02T05:00:19Z

Module Name

Sylvainjaume: /* Usage */

2010-05-02T04:59:54Z

Usage

Sylvainjaume: /* Authors, Collaborators & Contact */

2010-05-02T04:29:18Z

Authors, Collaborators & Contact

Sylvainjaume: /* Authors, Collaborators & Contact */

2010-05-02T04:29:00Z

Authors, Collaborators & Contact

Sylvainjaume: /* Authors, Collaborators & Contact */

2010-05-02T04:27:40Z

Authors, Collaborators & Contact

Sylvainjaume: /* Usage */

2010-05-02T04:26:03Z

Usage

@@ Line 25: / Line 25: @@
 * Sylvain Jaume: MIT CSAIL
 * Nicolas Rannou: ISEN IRISA
 * Ron Kikinis: Harvard Medical School SPL
 * Contact: [http://people.csail.mit.edu/sylvain sylvain at csail.mit.edu]

@@ Line 165: / Line 165: @@
 {|
+|
-* '''Step 15/24. :'''
+* '''Step 15/24. Click on the lower left tab to disable the overlay of the mask image:'''
 ** '''Input Image:''' input image
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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]]
 |}
 {|
+|
-* '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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']]
 |}
 {|
+|
-* '''Step 17/24. :'''
+* '''Step 17/24. Disable the overlay for the sagittal and coronal views:'''
 ** '''Input Image:''' input image
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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]]
 |}
 {|
+|
-* '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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]]
 |}
 {|
+|
-* '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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]]
 |}
 {|
+|
-* '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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]]
 |}
 {|
+|
-* '''Step 21/24. :'''
+* '''Step 21/24. Go to 'File' and 'Save' to save the output volume:'''
 ** '''Input Image:''' input image
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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']]
 |}
 {|
+|
-* '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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]]
 |}
 {|
+|
-* '''Step 23/24. :'''
+* '''Step 23/24. Click on the output directory to save to a different directory:'''
 ** '''Input Image:''' input image
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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]]
 |}
 {|
+|
-* '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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]]
 |}

@@ Line 8: / Line 8: @@
 {|
-|[[Image:MRI_Bias_Field_Correction_Slicer3_close_up.png|thumb|500px|MRIBiasFieldCorrection corrects for the intensity inhomogeneity in 3D MRI images.]]
+|[[Image:MRI_Bias_Field_Correction_Slicer3_close_up.png|thumb|500px|MRIBiasFieldCorrection corrects for the intensity inhomogeneity in 3D MRI images.
 |}

@@ Line 8: / Line 8: @@
 {|
-|[[Image:MRI_Bias_Field_Correction_Slicer3.png|thumb|500px|User Interface]]
+|[[Image:MRI_Bias_Field_Correction_Slicer3_close_up.png|thumb|500px|MRIBiasFieldCorrection corrects for the intensity inhomogeneity in 3D MRI images.]]
 |}

@@ Line 8: / Line 8: @@
 {|
-|[[Image:MRI_Bias_Field_Correction_Slicer3.png|thumb|280px|User Interface]]
+|[[Image:MRI_Bias_Field_Correction_Slicer3.png|thumb|500px|User Interface]]
 |}
 == General Information ==

@@ Line 39: / Line 39: @@
 {|
+|
-* '''Step 1/24. Select input image:'''
+* '''Step 1/24. To open the input image, click on 'File' and then 'Add Volume':'''
 ** '''Input Image:''' input image
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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 mask image:'''
+* '''Step 2/24. Select the input image and click Apply:'''
 ** '''Input Image:''' input image
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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
 ** '''Mask Image:''' label map providing an approximative segmentation of the ROI
 ** '''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]]
 |}

@@ Line 27: / Line 27: @@
 * Ron Kikinis: Harvard Medical School SPL
 * Contact: [http://people.csail.mit.edu/sylvain sylvain at csail.mit.edu]
-|[[Image:MIT_NAMIC_Logo.png|thumb|280px|This work was presented at the MIT NAMIC Week in 2009.]]
+|[[Image:MIT_NAMIC_Logo.png|thumb|380px|This work was presented at the MIT NAMIC Week in 2009.]]
 |}

@@ Line 34: / Line 34: @@
 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).
 {|