Modules:RegisterImagesMultiRes-Documentation-3.6 - Revision history

Gcasey at 17:34, 28 March 2010

2010-03-28T17:34:36Z

Gcasey at 17:25, 28 March 2010

2010-03-28T17:25:19Z

Gcasey: /* Module Name */

2010-03-28T17:24:10Z

Module Name

Gcasey: moved Modules:RegisterImagesMultiRes-Documentation-3.5 to Modules:RegisterImagesMultiRes-Documentation-3.6

2010-03-28T17:18:01Z

moved Modules:RegisterImagesMultiRes-Documentation-3.5 to Modules:RegisterImagesMultiRes-Documentation-3.6

Gcasey: /* Module Description */

2010-03-28T17:17:42Z

Module Description

Gcasey: /* References */

2010-03-28T17:16:39Z

References

Gcasey: /* Quick Tour of Features and Use */

2010-03-28T17:10:06Z

Quick Tour of Features and Use

Gcasey: /* Examples, Use Cases & Tutorials */

2010-03-28T17:08:31Z

Examples, Use Cases & Tutorials

Gcasey at 16:10, 5 February 2010

2010-02-05T16:10:28Z

Gcasey: Use blank slicer doc template

2010-02-05T14:53:03Z

Use blank slicer doc template

Show changes

← Older revision		Revision as of 17:34, 28 March 2010
Line 61:		Line 61:
	===Known bugs===		===Known bugs===

−	Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.	+	* [http://na-mic.org/Mantis/view.php?id=789 Box ROI is slow]
		+	* Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

@@ Line 1: / Line 1: @@
-[[Documentation-3.5|Return to Slicer 3.5 Documentation]]
+[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
-[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]
+[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]
 __NOTOC__

@@ Line 5: / Line 5: @@
 __NOTOC__
 ===Module Name===
-MyModule
+Register Images Robust Affine
 {|
-|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
+|[[Image:Fiducial_registration_before.jpg|thumb|280px|Images before alignment]]
-|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
+|[[Image:Fiducial_registration_after_multires.jpg|thumb|280px|Images after alignment]]
 |}

@@ Line 26: / Line 26: @@
 ===Module Description===
-Mutual information based affine registration using a multi-resolution optimization strategy.
+Mutual information based affine registration using a multi-resolution optimization strategy.  Several parts of the algorithm are based on a description of the FLIRT algorithm, see the Reference section.
 == Usage ==

← Older revision		Revision as of 17:16, 28 March 2010
Line 82:		Line 82:

	===References===		===References===
−	* ~~FSL Flirt~~	+	*The algorithm here is based on the description of the flirt algorithm as described below.
		+	*[http://www.fmrib.ox.ac.uk/analysis/research/flirt/]
		+	*M. Jenkinson and S.M. Smith. A global optimisation method for robust affine registration of brain images. Medical Image Analysis, 5(2):143-156, 2001.
		+	*M. Jenkinson, P.R. Bannister, J.M. Brady, and S.M. Smith. Improved optimisation for the robust and accurate linear registration and motion correction of brain images. NeuroImage, 17(2):825-841, 2002.

← Older revision	Revision as of 17:18, 28 March 2010
(No difference)

@@ Line 46: / Line 46: @@
 * '''Optional:'''
 ** Fixed Image Mask Image - A label image that is used to mask regions of interest in the fixed image.  The mask specified here is used to restrict the placement of samples in the fixed image used for optimizing the registration.  The user may want to mask the brain from background, mask everything in the brain except a lesion region, or otherwise specify the regions they would like to optimize in the registration.
 * '''Advanced:'''
 ** Number of iteration - Number of iterations to run at each stage of the optimization.  This method uses Fletcher-Reeves-Polak-Ribiere optimizer and the number of 1-D optimization is bounded by the number of iterations times the dimensionality of the transform.

@@ Line 33: / Line 33: @@
 ===Examples, Use Cases & Tutorials===
-* Note use cases for which this module is especially appropriate, and/or link to examples.
+* This module is intended to be a robust general-purpose mutual information affine registration tool
 ===Quick Tour of Features and Use===

@@ Line 16: / Line 16: @@
 ===Module Type & Category===
-Type: Interactive or CLI
+Type: CLI
-Category: Base or (Filtering, Registration, ''etc.'')
+Category: Registration
 ===Authors, Collaborators & Contact===
-* Author1: Affiliation & logo, if desired
+* Author1: Casey Goodlett, Kitware
-* Contributor1: Affiliation & logo, if desired
+* Contributor1: Dominik Meier, BWH
-* Contributor2: Affiliation & logo, if desired
+* Contact: Casey Goodlett
 ===Module Description===
-Overview of what the module does goes here.
+Mutual information based affine registration using a multi-resolution optimization strategy.
 == Usage ==
 ===Examples, Use Cases & Tutorials===
 * Note use cases for which this module is especially appropriate, and/or link to examples.
 ===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:'''
+* '''Required:'''
-* '''Parameters panel:'''
+** Fixed Image - Target image for registration.  The resulting transform will map the moving image to the fixed image.
-* '''Output panel:'''
+** Moving Image - Source image for registration.  The resulting transform will map the moving image to the fixed image.
-* '''Viewing panel:'''
+** Resample Image - Image node to create a resampled moving image.  The image node specified in this transform will store the result of resampling the moving image with computed transform.  Typically the user should select to create a new volume here.  This does not need to be specified, but the user should select either this option or output transform.
 == Development ==
@@ Line 49: / Line 56: @@
 ===Dependencies===
-Other modules or packages that are required for this module's use.
+* Editor, Threshold, Segmentation module: Useful for computing a label mask for the 'Fixed Image Mask Image' option.
 ===Known bugs===
@@ Line 65: / Line 72: @@
 Source code:
-*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
+*[http://viewvc.slicer.org/viewcvs.cgi/Applications/CLI/RegisterImagesModule/MultiResApplications/RegisterImagesMultiRes.cxx]
 == More Information ==
 ===Acknowledgment===
-Include funding and other support here.
+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. Information on the National Centers for Biomedical Computing can be obtained from National Centers for Biomedical Computing.
 ===References===
-Publications related to this module go here. Links to pdfs would be useful.
+* FSL Flirt