Modules:MRIBiasFieldCorrection-Documentation-3.5 - Revision history

Nicole: /* Source code & documentation */

2010-01-15T23:04:47Z

Source code & documentation

Sylvainjaume: /* Usage: add instructions for the visualization of the result */

2009-08-18T00:16:23Z

Usage: add instructions for the visualization of the result

Sylvainjaume: move instructions to the usage section

2009-08-18T00:06:53Z

move instructions to the usage section

Sylvainjaume: add usage instructions

2009-08-18T00:01:20Z

add usage instructions

Sylvainjaume: /* Source code & documentation */

2009-06-26T00:45:12Z

Source code & documentation

Sylvainjaume: /* MRI Bias Field Correction */

2009-06-26T00:44:08Z

MRI Bias Field Correction

Sylvainjaume: /* MRI Bias Field Correction */ remove old screenshots. The new ones showing the SPL Brain Atlas illustrate better the usage of the MRI Bias Field Correction module.

2009-06-20T21:39:09Z

MRI Bias Field Correction: remove old screenshots. The new ones showing the SPL Brain Atlas illustrate better the usage of the MRI Bias Field Correction module.

Sylvainjaume: /* MRI Bias Field Correction */ add screenshots of MRIBiasFieldCorrection module applied on the SPL 3D Brain Atlas

2009-06-20T21:36:49Z

MRI Bias Field Correction: add screenshots of MRIBiasFieldCorrection module applied on the SPL 3D Brain Atlas

Sylvainjaume: /* Authors, Collaborators & Contact */ add contact email

2009-06-20T21:13:43Z

Authors, Collaborators & Contact: add contact email

Sylvainjaume: /* Development */

2009-06-06T20:31:16Z

Development

@@ Line 100: / Line 100: @@
 * [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/MRIBiasFieldCorrection/ Source code]
-* [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Documentation generated by Doxygen]
+* [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Documentation generated by Doxygen]
 == More Information ==

@@ Line 54: / Line 54: @@
 * 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
+* Click on Apply.
 It took 32 min to process a 512x512x30 MRI volume on a MacBook laptop.
 ===Examples, Use Cases & Tutorials===

@@ Line 6: / Line 6: @@
 ===MRI Bias Field Correction===
 Filtering:MRIBiasFieldCorrection
 {|
-|[[Image:MRI_Bias_Field_Correction_Slicer3.png|thumb|560px|Screenshot of the MRIBiasFieldCorrection module in Slicer3.
+|[[Image:MRI_Bias_Field_Correction_Slicer3.png|thumb|560px|Screenshot of the MRIBiasFieldCorrection module in Slicer3 during development.
 The screenshot illustrates the application of the MRI Bias Field Correction on the SPL Atlas.
 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.
@@ Line 65: / Line 46: @@
 == Usage ==
-* Load the input dataset (Add Volume)
+* Load the input dataset (Main menu: Add Volume)
-* Go to the menu Modules > Filtering > MRI Bias Field Correction
+* Create a Mask Volume using the Editor (Modules > Editor) (the Threshold tool should give a good result)
-* Select the input dataset
+* Select the MRIBiasFieldCorrection module (Modules > Filtering > MRIBiasFieldCorrection)
-* Modify the number of iterations (large values make the processing longer)
+* In the left panel, select the Input Volume
-* Modify the fitting levels
+* Select the Mask Volume
-* Click on Apply (processing of large images take in the order of minutes)
+* In the Preview Volume menu , select 'Create New Volume'
-* Select the 'field' checkbox if you want to visualize the field
+* Do the same for the Output Volume menu
 ===Examples, Use Cases & Tutorials===

@@ Line 6: / Line 6: @@
 ===MRI Bias Field Correction===
 Filtering:MRIBiasFieldCorrection
 {|

@@ Line 86: / Line 86: @@
 ===Source code & documentation===
-* [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/N3MRIBiasFieldCorrection/ Source code]
+* [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/MRIBiasFieldCorrection/ Source code]
 * [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Documentation generated by Doxygen]

@@ Line 22: / Line 22: @@
 Note that the intensity inhomogeneity visible in the input image (left) has been corrected in the output image (right).]]
 |}
 == General Information ==

@@ Line 21: / Line 21: @@
 |[[Image:MRI_Bias_Field_Correction_Slicer3_close_up.png|thumb|560px|Close-up of the above screenshot showing the image before and after correction.
 Note that the intensity inhomogeneity visible in the input image (left) has been corrected in the output image (right).]]
 |}

@@ Line 22: / Line 22: @@
 * Nicolas Rannou: Harvard Medical School, Brigham and Women's Hospital
 * Sylvain Jaume: MIT Computer Science and Artificial Intelligence Laboratory
-* Contact: Nicolas Rannou <nrannou at bwh.harvard.edu>
+* Contact: <nrannou at bwh.harvard.edu>, <sylvain at csail.mit.edu>
 ===Module Description===

@@ Line 54: / Line 54: @@
 ===Dependencies===
-Other modules or packages that are required for this module's use.
+No other modules or packages are required to use this module.
 ===Known bugs===
@@ Line 64: / Line 65: @@
 Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.
 ===Source code & documentation===