Modules:SpineSegmentation-Documentation-3.6 - Revision history

Sylvainjaume: add link to HBM 2010 poster

2010-06-16T13:37:22Z

add link to HBM 2010 poster

Sylvainjaume: /* Source code & documentation */

2010-05-14T17:20:03Z

Source code & documentation

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

2010-05-14T06:37:46Z

Quick Tour of Features and Use

Sylvainjaume: /* Module Description */

2010-05-14T06:31:24Z

Module Description

Sylvainjaume: /* Tutorial */

2010-05-14T05:54:13Z

Tutorial

Sylvainjaume: /* Authors, Collaborators & Contact */

2010-05-14T05:51:28Z

Authors, Collaborators & Contact

Sylvainjaume: /* Module Name */

2010-05-14T05:44:14Z

Module Name

Sylvainjaume: /* Module Name */

2010-05-14T05:42:07Z

Module Name

Sylvainjaume: /* Tutorial */

2010-05-14T04:40:31Z

Tutorial

Sylvainjaume: /* Tutorial */

2010-05-14T04:38:06Z

Tutorial

← Older revision		Revision as of 13:37, 16 June 2010
Line 162:		Line 162:

	===References===		===References===
−	Stochastic Neurography, S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.	+	[http://people.csail.mit.edu/sylvain/Sylvain_Jaume_HBM_poster_2010.pdf Stochastic Neurography], S. Jaume, M. Loepprich, E.J. Schmidt, R. Kikinis, 16th Annual Meeting of the Organization for Human Brain Mapping (HBM 2010), Barcelona, Spain, June 6-10, 2010.

@@ Line 148: / Line 148: @@
 ===Source code & documentation===
-SpineSegmentation's source code (revision 151):
+Module source code (revision 151):
 *[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.cxx?annotate=151&root=sylvainproject SpineSegmentation.cxx]
 *[http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/SpineSegmentation.xml?annotate=151&root=sylvainproject SpineSegmentation.xml]
-Slicer's Doxygen documentation:
+Doxygen generated documentation:
-*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]
+*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html Slicer Doxygen]
 == More Information ==

@@ Line 111: / Line 111: @@
 ===Quick Tour of Features and Use===
 * '''Input panel:'''
-** '''Image input''' select the input image
+** '''Image input:''' select the input image
-** '''Image output''' create Slicer node for output image
+** '''Image output:''' create Slicer node for output image
-** '''Model output''' create Slicer node for output model
+** '''Model output:''' create Slicer node for output model
 * '''Command panel:'''
-** '''Default''' reset input and output nodes to blank values
+** '''Default:''' reset input and output nodes to blank values
-** '''Cancel''' cancel the execution of the algorithm
+** '''Cancel:''' cancel the execution of the algorithm
-** '''Apply''' apply the segmentation algorithm (takes approx. 3 min)
+** '''Apply:''' apply the segmentation algorithm (takes approx. 3 min)
 == Development ==

@@ Line 28: / Line 28: @@
 ===Module Description===
-Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module implements a model-based pattern recognition algorithm for fully automated segmentation.
+Image segmentation of the spinal cord and the cerebro-spinal fluid in T2-weighted MRI images. The SpineSegmentation module builds on Pattern Recognition theory to provide for a fully automated segmentation. The module first defines a shape model of the spinal cord modeling both the inner volume and the outer volume. Then the segmentation algorithm uses this model to explored the image space and find the best match given the field on intensities in the image. The advantage of this method relies on its unsupervised property: no need for any parameter setting or any initialization.
 == Usage ==

@@ Line 48: / Line 48: @@
 {|
+|
-|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|400px|0. download sample data]]
+|[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|600px|0. download sample data]]
 |}
 The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.
@@ Line 56: / Line 56: @@
 {|
+|
-|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|400px|1. load sample data]]
+|[[Image:SpineSegmentation_Slicer3.6_documentation01.png|thumb|600px|1. load sample data]]
 |}
@@ Line 62: / Line 62: @@
 {|
+|
-|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|400px|2. select SpineSegmentation module]]
+|[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|600px|2. select SpineSegmentation module]]
 |}
@@ Line 68: / Line 68: @@
 {|
+|
-|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|400px|3. select input image]]
+|[[Image:SpineSegmentation_Slicer3.6_documentation03.png|thumb|600px|3. select input image]]
 |}
@@ Line 74: / Line 74: @@
 {|
+|
-|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|400px|4. create image node]]
+|[[Image:SpineSegmentation_Slicer3.6_documentation04.png|thumb|600px|4. create image node]]
 |}
@@ Line 80: / Line 80: @@
 {|
+|
-|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|400px|5. create model node]]
+|[[Image:SpineSegmentation_Slicer3.6_documentation05.png|thumb|600px|5. create model node]]
 |}
@@ Line 86: / Line 86: @@
 {|
+|
-|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|400px|6. apply algorithm]]
+|[[Image:SpineSegmentation_Slicer3.6_documentation06.png|thumb|600px|6. apply algorithm]]
 |}
@@ Line 92: / Line 92: @@
 {|
+|
 The sliders on the top of each 2D view allows for reviewing the segmentation result overlaid on the input image.
 * Step 8/9. Save result image and model.
 {|
+|
 The output image and the 3D model can be saved using the Slicer user interface.
 * Step 9/9. Find contact information for help and paper reference.
 {|
+|
-|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|400px|9. help information]]
+|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|600px|9. help information]]
 |}

@@ Line 23: / Line 23: @@
 * Sylvain Jaume: MIT CSAIL
 * Contact: sylvain at csail.mit.edu
 ===Module Description===

@@ Line 10: / Line 10: @@
 |[[Image:SpineSegmentation_Slicer3.6_documentation00.png|thumb|300px|A sample data set is available on http://nitrc.org. Download both .mhd and .zraw files.]]
 |[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]
-|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]
+|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|After 3 minutes, the segmentation results appear: a label map (blue) and a 3D model (3D view).]]
 |}

@@ Line 5: / Line 5: @@
 __NOTOC__
 ===Module Name===
-SpineSegmentation module for Slicer 3.6
+SpineSegmentation module for Slicer 3.6 (available through Slicer extension manager)
 {|
 |[[Image:SpineSegmentation_Slicer3.6_documentation02.png|thumb|300px|The SpineSegmentation module is available through the Slicer extension module manager.]]
-|[[Image:SpineSegmentation_Slicer3.6_documentation07.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]
+|[[Image:SpineSegmentation_Slicer3.6_documentation09.png|thumb|300px|In 3 minutes of processing, a label map (blue) and a 3D model (3D view) are displayed.]]
 |}

@@ Line 40: / Line 40: @@
 ===Tutorial===
-* Step 0. Download Sample Data
+* Step 0/9. Download Sample Data
 The sample data sets MRI_Spine.mhd and MRI_Spine.zraw are available at the link below. You will need to create a username on http://nitrc.org. Then log onto nitrc.org and click on the link below. Right-click on MRI_Spine.mhd and MRI_Spine.zraw to copy those files to your local directory.
   http://www.nitrc.org/plugins/scmsvn/viewcvs.php/Slicer3/Modules/SpineSegmentation/TestingData/?root=sylvainproject
-Below are the step-by-step instructions to load, process and save some sample data (see link above).
+* Step 1/9. Load the sample data
 {|
+|