Modules:EMSegment-TemplateBuilder:EMSegment-TemplateBuilder-Steps - Revision history

Fedorov: /* (7/9) Edit Node-based Parameters: Specify node-based segmentation parameters */

2009-07-17T20:39:08Z

(7/9) Edit Node-based Parameters: Specify node-based segmentation parameters

Fedorov: /* (7/9) Edit Node-based Parameters: Specify node-based segmentation parameters */

2009-07-17T20:38:39Z

(7/9) Edit Node-based Parameters: Specify node-based segmentation parameters

Yumin: /* Generate EM Segmentation Result Gallery */

2009-03-24T18:18:40Z

Generate EM Segmentation Result Gallery

Yumin at 18:14, 19 March 2009

2009-03-19T18:14:38Z

Yumin at 18:05, 19 March 2009

2009-03-19T18:05:46Z

Yumin: /* (6/9) Specify Intensity Distributions: Define intensity distribution for each anatomical structure */

2009-03-19T17:59:49Z

(6/9) Specify Intensity Distributions: Define intensity distribution for each anatomical structure

Yumin at 17:48, 19 March 2009

2009-03-19T17:48:30Z

Yumin: New page: = EMSegment Template Builder Workflow Wizard Steps= == (1/9)Define Parameters Set: Select parameter set or create new parameters == [[Image:EMSegment-Workflow-1-9.png|thumb|580px|Step 1/9...

2009-03-19T17:19:19Z

New page: = EMSegment Template Builder Workflow Wizard Steps= == (1/9)Define Parameters Set: Select parameter set or create new parameters == [[Image:EMSegment-Workflow-1-9.png|thumb|580px|Step 1/9...

New page

= EMSegment Template Builder Workflow Wizard Steps=

== (1/9)Define Parameters Set: Select parameter set or create new parameters ==
[[Image:EMSegment-Workflow-1-9.png|thumb|580px|Step 1/9]]
* For now, use tutorial set
* Later use this interface to create a new parameter set
 

== (2/9)Define Hierarchy: Define a hierarchy of anatomical structures ==
[[Image:EMSegment-Workflow-2-9.png|thumb|580px|Step 2/9]]
* Right click to add or delete nodes
* Label corresponds to eventual voxel values in segmentation result
 

== (3/9)Assign Atlas: Assign atlases for anatomical structures ==
[[Image:EMSegment-Workflow-3-9.png|thumb|580px|Step 3/9]]
 

== (4/9)Select Target Images: Choose the set of images that will be segmented ==
[[Image:EMSegment-Workflow-4-9.png|thumb|580px|Step 4/9]]
 

== (5/9)Intensity Normalization: Normalize target images ==
[[Image:EMSegment-Workflow-5-9.png|thumb|580px|Step 5/9]]
 

== (6/9)Specify Intensity Distributions: Define intensity distribution for each anatomical structure ==
[[Image:EMSegment-Workflow-6-9.png|thumb|580px|Step 6/9]]
 

== (7/9)Edit Node-based Parameters: Specify node-based segmentation parameters ==
[[Image:EMSegment-Workflow-7-9.png|thumb|580px|Step 7/9]]
 

== (8/9)Edit Registration Parameters: Specify atlas-to-target registration parameters ==
[[Image:EMSegment-Workflow-8-9.png|thumb|580px|Step 8/9]]
 

== (9/9)Run Segmentation: Save work and apply EM Algorithm to segment target images ==
[[Image:EMSegment-Workflow-9-9.png|thumb|580px|Step 9/9]]
 

= Generate EM Segmentation Result Gallery =

== Select the first target volume for display==
== Select the segmentation results volume in the Labelmap chooser==
== Adjust opacity of the labelmap==
== (Optional) Generate and display surfaces from the segmentation results==

1. Select the "Model Generation" -> "Model Maker" module
2. For "Input Volume", select the $My_Segmentation_Result
3. For "Output Directory", create and select $PLAYPEN_DIR/Models
4. For "Model Scene File", select $PLAYPEN_DIR/Models.mrml
5. Enable "Generate All Models"
6. Set "End Label" to the highest label that you produced (e.g., 8 fro the tutorial)
7. Enable "Joint Smoothing"
8. Click on Apply (this will generate the models and will take approximately 5 minutes)
9. Load the models into Slicer (File->Import Scene; select $PLAYPEN_DIR/Models.mrml)
10. Use The Models module to manipulate display attributes

<gallery>
Image:EMSVisualizeTutorialResultsData.png|EMSegmenter Applied to MR T1 & T2 tutorial data
Image:EMSegment31Structures.png|Segmentation of brain structures using EMSegmenter
</gallery>

@@ Line 64: / Line 64: @@
 * Influence
 ** Prior weight relative to other structures
 ** Atlas
 ** Input channels
 ** Smoothing (parent nodes only)
 * Stopping Conditions
 <br style="clear:both;"/>

@@ Line 68: / Line 68: @@
 ** Smoothing (parent nodes only)
 * Stopping Conditions
 <br style="clear:both;"/>

@@ Line 90: / Line 90: @@
 * Adjust opacity of the label map
 * (Optional) Generate and display surfaces from the segmentation results
-# Select the "Model Generation" -> "Model Maker" module
+# Select the "Surface Models" -> "Model Maker" module
 # For "Input Volume", select the $My_Segmentation_Result
 # For "Output Directory", create and select $PLAYPEN_DIR/Models

@@ Line 4: / Line 4: @@
 == (1/9) Define Parameters Set: Select parameter set or create new parameters ==
-[[Image:EMSegment-Workflow-1-9.png|thumb|580px|Step 1/9]]
+[[Image:EMSegment-Workflow-1-9.png|thumb|300px|Step 1/9]]
   * For now, use tutorial set
   * Later use this interface to create a new parameter set
@@ Line 10: / Line 10: @@
 == (2/9) Define Hierarchy: Define a hierarchy of anatomical structures ==
-[[Image:EMSegment-Workflow-2-9.png|thumb|580px|Step 2/9]]
+[[Image:EMSegment-Workflow-2-9.png|thumb|300px|Step 2/9]]
   * Right click to add or delete nodes
   * Label corresponds to eventual voxel values in segmentation result
@@ Line 16: / Line 16: @@
 == (3/9) Assign Atlas: Assign atlases for anatomical structures ==
-[[Image:EMSegment-Workflow-3-9.png|thumb|580px|Step 3/9]]
+[[Image:EMSegment-Workflow-3-9.png|thumb|300px|Step 3/9]]
 * To change or add new atlas volumes: Load new volumes into Slicer3, then Select new volumes at this step
 <br style="clear:both;"/>
 == (4/9) Select Target Images: Choose the set of images that will be segmented ==
-[[Image:EMSegment-Workflow-4-9.png|thumb|580px|Step 4/9]]
+[[Image:EMSegment-Workflow-4-9.png|thumb|300px|Step 4/9]]
 * To change or add new atlas volumes: Load new volumes into Slicer3, then Select new volumes at this step
 * You can reorder target images; order is important
@@ Line 33: / Line 33: @@
 * Simple, default strategy
 * Default parameter sets available from pulldown
-[[Image:EMSegment-Workflow-5-9.png|thumb|580px|Step 5/9]]
+[[Image:EMSegment-Workflow-5-9.png|thumb|300px|Step 5/9]]
 <br style="clear:both;"/>
 == (6/9) Specify Intensity Distributions: Define intensity distribution for each anatomical structure ==
 {|
-|[[Image:EMSegment-Workflow-6-9.png|thumb|580px|Step 6/9]]
+|[[Image:EMSegment-Workflow-6-9.png|thumb|300px|Step 6/9]]
-|[[Image:EMSegment-Workflow-6-9-sample.png|thumb|580px|Step 6/9 - Sample Voxels]]
+|[[Image:EMSegment-Workflow-6-9-sample.png|thumb|300px|Step 6/9 - Sample Voxels]]
-|[[Image:EMSegment-Workflow-6-9-sample-remove.png|thumb|580px|Step 6/9 - Remove Voxels]]
+|[[Image:EMSegment-Workflow-6-9-sample-remove.png|thumb|300px|Step 6/9 - Remove Voxels]]
 |}
 * Intensity distributions define appearance of each leaf structure
@@ Line 60: / Line 60: @@
 == (7/9) Edit Node-based Parameters: Specify node-based segmentation parameters ==
-[[Image:EMSegment-Workflow-7-9.png|thumb|580px|Step 7/9]]
+[[Image:EMSegment-Workflow-7-9.png|thumb|300px|Step 7/9]]
 * Segmentation parameters for every tree node
 * Influence
@@ Line 71: / Line 71: @@
 == (8/9) Edit Registration Parameters: Specify atlas-to-target registration parameters ==
-[[Image:EMSegment-Workflow-8-9.png|thumb|580px|Step 8/9]]
+[[Image:EMSegment-Workflow-8-9.png|thumb|300px|Step 8/9]]
 * Moving image registered to first target image (You can choose any image loaded into Slicer3)
 * Same transformation applied to all atlas images before segmentation begins
@@ Line 77: / Line 77: @@
 ==(9/9) Run Segmentation: Save work and apply EM Algorithm to segment target images==
-[[Image:EMSegment-Workflow-9-9.png|thumb|580px|Step 9/9]]
+[[Image:EMSegment-Workflow-9-9.png|thumb|300px|Step 9/9]]
 * Select output and run registration
 * You can troubleshoot preprocessing by saving intermediate results

@@ Line 1: / Line 1: @@
 = EMSegment Template Builder Workflow Wizard Steps=
@@ Line 19: / Line 21: @@
 == (4/9) Select Target Images: Choose the set of images that will be segmented ==
 * To change or add new atlas volumes: Load new volumes into Slicer3, then Select new volumes at this step
 * You can reorder target images; order is important
@@ Line 24: / Line 27: @@
 * First target is fixed image
 * Rigid, mutual information registration
 <br style="clear:both;"/>
@@ Line 35: / Line 37: @@
 == (6/9) Specify Intensity Distributions: Define intensity distribution for each anatomical structure ==
 * Intensity distributions define appearance of each leaf structure
 * Gaussian
@@ Line 50: / Line 57: @@
 * Tip: sample first, then fine tune manually
 <br style="clear:both;"/>
 == (7/9) Edit Node-based Parameters: Specify node-based segmentation parameters ==
 * Segmentation parameters for every tree node
 * Influence
@@ Line 66: / Line 68: @@
 ** Smoothing (parent nodes only)
 * Stopping Conditions
 <br style="clear:both;"/>
 == (8/9) Edit Registration Parameters: Specify atlas-to-target registration parameters ==
 * Moving image registered to first target image (You can choose any image loaded into Slicer3)
 * Same transformation applied to all atlas images before segmentation begins
 <br style="clear:both;"/>
 ==(9/9) Run Segmentation: Save work and apply EM Algorithm to segment target images==
 * Select output and run registration
 * You can troubleshoot preprocessing by saving intermediate results
 * Choose an output labelmap
 * ROI governs segmentation processing (one-based, not zero-based)
 <br style="clear:both;"/>
@@ Line 106: / Line 106: @@
 Image:EMSegment31Structures.png|Segmentation of brain structures using EMSegmenter
 </gallery>

@@ Line 39: / Line 39: @@
 * Dimensionality equal to number of target images
 * Two methods
 ** Sample voxels from images
-[[Image:EMSegment-Workflow-6-9-sample.png|thumb|580px|Step 6/9 - Sample Voxels]] [[Image:EMSegment-Workflow-6-9-sample-remove.png|thumb|580px|Step 6/9 - Remove Voxels]]
-*** Load first target image into Slicer3 slicer view
+# Load first target image into Slicer3 slicer view
-*** Choose anatomical structure
+# Choose anatomical structure
-*** Choose `manual sampling’
+# Choose `manual sampling’
-*** Ctrl-left-click on image to add voxels
+# Ctrl-left-click on image to add voxels
-*** To remove an unwanted sample right-click on it and choose “remove”
+# To remove an unwanted sample right-click on it and choose “remove”
-*** Change back to “manual” mode to tweak distribution
+# Change back to “manual” mode to tweak distribution
-** Specify mean and covariance manually
 * Tip: sample first, then fine tune manually
 <br style="clear:both;"/>