Slicer Wiki - User contributions [en]

Modules:EMSegment-Simple-3.4

2009-03-27T15:52:49Z

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

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
EM Segment Simple
{|
|[[Image:EMSegment-Simple.png|thumb|580px|EM Segment Simple module GUI and Result]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Brad Davis: Kitware, Inc.
* Kilian Pohl: IBM
* Sebastien Barre: Kitware, Inc.
* Yumin Yuan: Kitware, Inc.
* Polina Golland: MIT
* Contact: Brad Davis, brad.davis@kitware.com

===Module Description===
This module provide a simplified "one-click" GUI interface for the '''EMSegment Command-line Executable'''. The interface is simple because the number of required command-line parameters is minimized, and it is flexible because any EM algorithm parameter can be modified, within the MRML scene, via the EMSegment GUI interface.

== Usage ==
Similar to the '''EMSegment Command-line Executable''', once a set of parameters for segmentation algorithm is deemed satisfactory through the process of calibrating in the '''Template Builder''' module, the user will commonly want to bypass this detailed calibration process when segmenting new images. This module provides a simple interface to specify a small number of required command-line parameters --- a MRML scene (containing algorithm parameters), a target image (or multiple target images, e.g., T1 and T2), and an output labelmap image --- , and to allow any EM algorithm parameters to be modified, within the MRML scene, via the EMSegment GUI interface.

===Examples, Use Cases & Tutorials===
* A full Tutorial for all three EMSegment modules

These slides and data describe the Slicer3 implementation of all three EMSegment modules and demonstrate their use. A recent (later than 7Jan08) version of Slicer3 is required to run the test data.

[[Media:EMSegTutorial-AHM2008.ppt | Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Data]]

===Quick Tour of Features and Use===

* '''Parameters panel:''' [[Image:EMSegment-Simple-Panel.png|300px|thumb|EMSegment Simple Parameters Panel]]
** MRML Scene: Select the mrml scene for the tutorial parameter set
** Result Labelmap: Select a new image filename for output labelmap
** Target Volumes: Select input target volumes (Note: target volume order is important)
** Click `Apply’, wait (~30 minutes for full size images)

== Development ==
The module is implemented as a very simple programmatic Slicer3 module, whose purpose is to offer simple interface for segmenting new data
with predefined parameter set. The module GUI interacts with the Logic classes, which are solely responsible for maintaining and accessing MRML nodes. The
Logic class provides APIs that the GUI code uses to access and modify data. The Logic class also wraps the algorithm code itself.

===Dependencies===

Slicer3 base modules.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems.
*Atlas-to-target registration and intensity normalization are very important; it will be most effective to apply these steps using algorithms that are customized to your data. Defaults are provided but they may perform poorly for your data---this will lead to poor segmentation results.

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===

[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ Links] for the module.
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]
*API: [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentMRMLManager.html MRML Manager] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentLogic.html Module Logic] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentGUI.html Module GUI]

== More Information ==

For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]

The old [[Modules:EM-Segmenter-Documentation:FAQ |EMSegmenter FAQ]] contains frequently asked questions about the EMSegment interfaces in Slicer3.

There is also an old [http://www.na-mic.org/Wiki/index.php/EMSegmenter_Mini-Tutorials EMSegmenter Mini-Tutorials]

===Acknowledgment===
Funding for the EMSegmenter module was provided by NAMIC.

===References===

Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212.
[[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]

File:EMSegment-CL-Panel.png

2009-03-27T15:47:44Z

Yumin:

Modules:EMSegment-TemplateBuilder:EMSegment-TemplateBuilder-Steps

2009-03-24T18:18:40Z

Yumin: /* Generate EM Segmentation Result Gallery */

[[Modules:EMSegment-TemplateBuilder|Return to EMSegment Template Builder Documentation]]

= 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|300px|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|300px|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|300px|Step 3/9]]
* To change or add new atlas volumes: Load new volumes into Slicer3, then Select new volumes at this step
 

== (4/9) Select Target Images: Choose the set of images that will be segmented ==
[[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
* You can choose to align target images
* First target is fixed image
* Rigid, mutual information registration
 

== (5/9) Intensity Normalization: Normalize target images ==
* You can choose to normalize target images
* Simple, default strategy
* Default parameter sets available from pulldown
[[Image:EMSegment-Workflow-5-9.png|thumb|300px|Step 5/9]]
 

== (6/9) Specify Intensity Distributions: Define intensity distribution for each anatomical structure ==
{|
|[[Image:EMSegment-Workflow-6-9.png|thumb|300px|Step 6/9]]
|[[Image:EMSegment-Workflow-6-9-sample.png|thumb|300px|Step 6/9 - Sample Voxels]]
|[[Image:EMSegment-Workflow-6-9-sample-remove.png|thumb|300px|Step 6/9 - Remove Voxels]]
|}
* Intensity distributions define appearance of each leaf structure
* Gaussian
* Dimensionality equal to number of target images
* Two methods
** Specify mean and covariance manually
** Sample voxels from images

# Load first target image into Slicer3 slicer view
# Choose anatomical structure
# Choose `manual sampling’
# Ctrl-left-click on image to add voxels
# To remove an unwanted sample right-click on it and choose “remove”
# Change back to “manual” mode to tweak distribution

* Tip: sample first, then fine tune manually
 

== (7/9) Edit Node-based Parameters: Specify node-based segmentation parameters ==
[[Image:EMSegment-Workflow-7-9.png|thumb|300px|Step 7/9]]
* Segmentation parameters for every tree node
* Influence
** Prior weight relative to other structures
** Atlas
** Input channels
** Smoothing (parent nodes only)
* Stopping Conditions
 

== (8/9) Edit Registration Parameters: Specify atlas-to-target registration parameters ==
[[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
 

==(9/9) Run Segmentation: Save work and apply EM Algorithm to segment target images==
[[Image:EMSegment-Workflow-9-9.png|thumb|300px|Step 9/9]]
* 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)
 

= 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 label map
* (Optional) Generate and display surfaces from the segmentation results
# Select the "Surface Models" -> "Model Maker" module
# For "Input Volume", select the $My_Segmentation_Result
# For "Output Directory", create and select $PLAYPEN_DIR/Models
# For "Model Scene File", select $PLAYPEN_DIR/Models.mrml
# Enable "Generate All Models"
# Set "End Label" to the highest label that you produced (e.g., 8 fro the tutorial)
# Enable "Joint Smoothing"
# Click on Apply (this will generate the models and will take approximately 5 minutes)
# Load the models into Slicer (File->Import Scene; select $PLAYPEN_DIR/Models.mrml)
# 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>

[[Modules:EMSegment-TemplateBuilder|Return to EMSegment Template Builder Documentation]]

Modules:EMSegment-TemplateBuilder:EMSegment-TemplateBuilder-Steps

2009-03-19T18:14:38Z

2009-03-19T18:05:46Z

Yumin:

[[Modules:EMSegment-TemplateBuilder|Return to EMSegment Template Builder Documentation]]

= 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]]
* To change or add new atlas volumes: Load new volumes into Slicer3, then Select new volumes at this step
 

== (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]]
* 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
* You can choose to align target images
* First target is fixed image
* Rigid, mutual information registration
 

== (5/9) Intensity Normalization: Normalize target images ==
* You can choose to normalize target images
* Simple, default strategy
* Default parameter sets available from pulldown
[[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]]
|[[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]]
|}
* Intensity distributions define appearance of each leaf structure
* Gaussian
* Dimensionality equal to number of target images
* Two methods
** Specify mean and covariance manually
** Sample voxels from images

# Load first target image into Slicer3 slicer view
# Choose anatomical structure
# Choose `manual sampling’
# Ctrl-left-click on image to add voxels
# To remove an unwanted sample right-click on it and choose “remove”
# Change back to “manual” mode to tweak distribution

* Tip: sample first, then fine tune manually
 

== (7/9) Edit Node-based Parameters: Specify node-based segmentation parameters ==
[[Image:EMSegment-Workflow-7-9.png|thumb|580px|Step 7/9]]
* Segmentation parameters for every tree node
* Influence
** Prior weight relative to other structures
** Atlas
** Input channels
** Smoothing (parent nodes only)
* Stopping Conditions
 

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

==(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]]
* 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)
 

= 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 label map
* (Optional) Generate and display surfaces from the segmentation results
# Select the "Model Generation" -> "Model Maker" module
# For "Input Volume", select the $My_Segmentation_Result
# For "Output Directory", create and select $PLAYPEN_DIR/Models
# For "Model Scene File", select $PLAYPEN_DIR/Models.mrml
# Enable "Generate All Models"
# Set "End Label" to the highest label that you produced (e.g., 8 fro the tutorial)
# Enable "Joint Smoothing"
# Click on Apply (this will generate the models and will take approximately 5 minutes)
# Load the models into Slicer (File->Import Scene; select $PLAYPEN_DIR/Models.mrml)
# 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>

[[Modules:EMSegment-TemplateBuilder|Return to EMSegment Template Builder Documentation]]

Modules:EMSegment-TemplateBuilder:EMSegment-TemplateBuilder-Steps

2009-03-19T17:59:49Z

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

= 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]]
* To change or add new atlas volumes: Load new volumes into Slicer3, then Select new volumes at this step
 

== (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
* You can choose to align target images
* First target is fixed image
* Rigid, mutual information registration
[[Image:EMSegment-Workflow-4-9.png|thumb|580px|Step 4/9]]
 

== (5/9) Intensity Normalization: Normalize target images ==
* You can choose to normalize target images
* Simple, default strategy
* Default parameter sets available from pulldown
[[Image:EMSegment-Workflow-5-9.png|thumb|580px|Step 5/9]]
 

== (6/9) Specify Intensity Distributions: Define intensity distribution for each anatomical structure ==
* Intensity distributions define appearance of each leaf structure
* Gaussian
* Dimensionality equal to number of target images
* Two methods
** Specify mean and covariance manually
** Sample voxels from images

# Load first target image into Slicer3 slicer view
# Choose anatomical structure
# Choose `manual sampling’
# Ctrl-left-click on image to add voxels
# To remove an unwanted sample right-click on it and choose “remove”
# Change back to “manual” mode to tweak distribution

* Tip: sample first, then fine tune manually
{|
|[[Image:EMSegment-Workflow-6-9.png|thumb|580px|Step 6/9]]
|[[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]]
|}

 

== (7/9) Edit Node-based Parameters: Specify node-based segmentation parameters ==
* Segmentation parameters for every tree node
* Influence
** Prior weight relative to other structures
** Atlas
** Input channels
** Smoothing (parent nodes only)
* Stopping Conditions
[[Image:EMSegment-Workflow-7-9.png|thumb|580px|Step 7/9]]
 

== (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
[[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==
* 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)

[[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 label map
* (Optional) Generate and display surfaces from the segmentation results
# Select the "Model Generation" -> "Model Maker" module
# For "Input Volume", select the $My_Segmentation_Result
# For "Output Directory", create and select $PLAYPEN_DIR/Models
# For "Model Scene File", select $PLAYPEN_DIR/Models.mrml
# Enable "Generate All Models"
# Set "End Label" to the highest label that you produced (e.g., 8 fro the tutorial)
# Enable "Joint Smoothing"
# Click on Apply (this will generate the models and will take approximately 5 minutes)
# Load the models into Slicer (File->Import Scene; select $PLAYPEN_DIR/Models.mrml)
# 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>

Modules:EMSegment-TemplateBuilder:EMSegment-TemplateBuilder-Steps

2009-03-19T17:48:30Z

Yumin:

= 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]]
* To change or add new atlas volumes: Load new volumes into Slicer3, then Select new volumes at this step
 

== (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
* You can choose to align target images
* First target is fixed image
* Rigid, mutual information registration
[[Image:EMSegment-Workflow-4-9.png|thumb|580px|Step 4/9]]
 

== (5/9) Intensity Normalization: Normalize target images ==
* You can choose to normalize target images
* Simple, default strategy
* Default parameter sets available from pulldown
[[Image:EMSegment-Workflow-5-9.png|thumb|580px|Step 5/9]]
 

== (6/9) Specify Intensity Distributions: Define intensity distribution for each anatomical structure ==
* Intensity distributions define appearance of each leaf structure
* Gaussian
* 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
*** Choose anatomical structure
*** Choose `manual sampling’
*** Ctrl-left-click on image to add voxels
*** To remove an unwanted sample right-click on it and choose “remove”
*** Change back to “manual” mode to tweak distribution
** Specify mean and covariance manually
* Tip: sample first, then fine tune manually

[[Image:EMSegment-Workflow-6-9.png|thumb|580px|Step 6/9]]
 

== (7/9) Edit Node-based Parameters: Specify node-based segmentation parameters ==
* Segmentation parameters for every tree node
* Influence
** Prior weight relative to other structures
** Atlas
** Input channels
** Smoothing (parent nodes only)
* Stopping Conditions
[[Image:EMSegment-Workflow-7-9.png|thumb|580px|Step 7/9]]
 

== (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
[[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==
* 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)

[[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 label map
* (Optional) Generate and display surfaces from the segmentation results
# Select the "Model Generation" -> "Model Maker" module
# For "Input Volume", select the $My_Segmentation_Result
# For "Output Directory", create and select $PLAYPEN_DIR/Models
# For "Model Scene File", select $PLAYPEN_DIR/Models.mrml
# Enable "Generate All Models"
# Set "End Label" to the highest label that you produced (e.g., 8 fro the tutorial)
# Enable "Joint Smoothing"
# Click on Apply (this will generate the models and will take approximately 5 minutes)
# Load the models into Slicer (File->Import Scene; select $PLAYPEN_DIR/Models.mrml)
# 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>

Modules:EMSegment-TemplateBuilder:EMSegment-TemplateBuilder-Steps

2009-03-19T17:19:19Z

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...

Modules:EMSegment-TemplateBuilder-3.4

2009-03-19T16:25:21Z

Yumin:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
EM Segment Template Builder

{|
|[[Image:EMSegment-Workflow.png|thumb|580px|EM Segment Workflow]]
|[[Image:EMSegment-Template.png|thumb|580px|EM Segment Template Builder GUI and EM Segment Result]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Segmentation

===Authors, Collaborators & Contact===
* Kilian Pohl: Harvard/BWH
* Brad Davis: Kitware, Inc.
* Sebastien Barre: Kitware, Inc.
* Yumin Yuan: Kitware, Inc.
* Polina Golland: MIT
* Contact: Brad Davis, brad.davis@kitware.com

===Module Description===
The EMSegment template builder module is the primary Slicer3 interface to the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. The target audience for this module is someone familiar with brain atlases and tissue labels, not a computer scientist. It allows the user to configure the algorithm---step-by-step---to a variety of imaging protocols and anatomical structures, and then apply the algorithm to segment data. Configuration settings are stored in an EMSegment parameters node in the Slicer3 MRML tree. These settings can be saved and later applied to new data via any of the EMSegment interfaces within Slicer3 or the command-line EMSegment executable.

== Usage ==

The purpose of the module is to configure the algorithm to automatically segment anatomical structures in medical images. First the user has to specify parameters defining the image protocol and the anatomical structures of interests. This process results in a template that the module uses to automatically segment large data sets. The template is composed of atlas data and a non-trivial collection of parameters for the EMSegment algorithm.

Once the parameters are specified, the target images are segmented
using the EM Segmentation algorithm (Pohl et al.). If the results are
satisfactory, the template is saved and can be used later to segment
new images (via the GUI or batch processing). If the results are
unsatisfactory, the parameters can be modified and the segmentation
re-run.

One important aspect of the project is the workflow wizard. This
wizard simplifies the module by dividing the complicated template
specification task into a number of smaller, intuitive steps.

===Examples, Use Cases & Tutorials===
* A full Tutorial for all three EMSegment modules

These slides and data describe the Slicer3 implementation of all three EMSegment modules and demonstrate their use. A recent (later than 7Jan08) version of Slicer3 is required to run the test data.

[[Media:EMSegTutorial-AHM2008.ppt | Tutorial Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Tutorial Data]]

* Another detailed training tutorial on EM Segment algorithm and Slicer3 EMSegment Template Builder module
[http://wiki.na-mic.org/Wiki/images/2/2f/AutomaticSegmentation_SoniaPujol_Munich2008.ppt Tutorial Slides] - [http://wiki.na-mic.org/Wiki/images/b/b7/AutomaticSegmentation.tar.gz Training Data]

===Quick Tour of Features and Use===
There is a [[Modules:EMSegment-TemplateBuilder:EMSegment-TemplateBuilder-Steps | step-by-step instruction]] with screen shots to describe the Workflow Wizard interface.
Here is the brief version of the steps in the wizard:

*1/9 Define Parameters Set: Select parameter set or create new parameters
*2/9 Define Hierarchy: Define a hierarchy of anatomical structures
*3/9 Assign Atlas: Assign atlases for anatomical structures
*4/9 Select Target Images: Choose the set of images that will be segmented
*5/9 Intensity Normalization: Normalize target images
*6/9 Specify Intensity Distributions: Define intensity distribution for each anatomical structure
*7/9 Edit Node-based Parameters: Specify node-based segmentation parameters
*8/9 Edit Registration Parameters: Specify atlas-to-target registration parameters
*9/9 Run Segmentation: Save work and apply EM Algorithm to segment target images

== Development ==

The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]

The module is implemented as a programmatic Slicer3 module because it
requires a large degree of interaction with the user, the data stored
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node
structure is rather complicated (for example the anatomical tissue
hierarchy and a large number of interdependent nodes) the Logic class
is solely responsible for maintaining and accessing these nodes. The
Logic class provides an API that the GUI code uses to access and
modify data. The Logic class also wraps the algorithm code itself.

===Dependencies===

Slicer3 base modules.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems.
*Atlas-to-target registration and intensity normalization are very important; it will be most effective to apply these steps using algorithms that are customized to your data. Defaults are provided but they may perform poorly for your data---this will lead to poor segmentation results.

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===

[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ Links] for the module.
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]
*API: [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentMRMLManager.html MRML Manager] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentLogic.html Module Logic] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentGUI.html Module GUI]

== More Information ==
*Some background materials: [http://wiki.na-mic.org/Wiki/index.php/EMSegmenter EMSegmenter history]
*For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]
*The old [[Modules:EM-Segmenter-Documentation:FAQ |EMSegmenter FAQ]] contains frequently asked questions about the EMSegment interfaces in Slicer3.
*There is also an old [http://www.na-mic.org/Wiki/index.php/EMSegmenter_Mini-Tutorials EMSegmenter Mini-Tutorials]

===Acknowledgment===
Funding for the EMSegmenter module was provided by NAMIC.

===References===
Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212.
[[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]

Modules:EMSegment-TemplateBuilder-3.4

2009-03-19T16:16:05Z

Yumin:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
EM Segment Template Builder

{|
|[[Image:EMSegment-Workflow.png|thumb|580px|EM Segment Workflow]]
|[[Image:EMSegment-Template.png|thumb|580px|EM Segment Template Builder GUI and EM Segment Result]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Segmentation

===Authors, Collaborators & Contact===
* Kilian Pohl: Harvard/BWH
* Brad Davis: Kitware, Inc.
* Sebastien Barre: Kitware, Inc.
* Yumin Yuan: Kitware, Inc.
* Polina Golland: MIT
* Contact: Brad Davis, brad.davis@kitware.com

===Module Description===
The EMSegment template builder module is the primary Slicer3 interface to the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. The target audience for this module is someone familiar with brain atlases and tissue labels, not a computer scientist. It allows the user to configure the algorithm---step-by-step---to a variety of imaging protocols and anatomical structures, and then apply the algorithm to segment data. Configuration settings are stored in an EMSegment parameters node in the Slicer3 MRML tree. These settings can be saved and later applied to new data via any of the EMSegment interfaces within Slicer3 or the command-line EMSegment executable.

== Usage ==

The purpose of the module is to configure the algorithm to automatically segment anatomical structures in medical images. First the user has to specify parameters defining the image protocol and the anatomical structures of interests. This process results in a template that the module uses to automatically segment large data sets. The template is composed of atlas data and a non-trivial collection of parameters for the EMSegment algorithm.

Once the parameters are specified, the target images are segmented
using the EM Segmentation algorithm (Pohl et al.). If the results are
satisfactory, the template is saved and can be used later to segment
new images (via the GUI or batch processing). If the results are
unsatisfactory, the parameters can be modified and the segmentation
re-run.

One important aspect of the project is the workflow wizard. This
wizard simplifies the module by dividing the complicated template
specification task into a number of smaller, intuitive steps.

===Examples, Use Cases & Tutorials===
* A full Tutorial for all three EMSegment modules

These slides and data describe the Slicer3 implementation of all three EMSegment modules and demonstrate their use. A recent (later than 7Jan08) version of Slicer3 is required to run the test data.

[[Media:EMSegTutorial-AHM2008.ppt | Tutorial Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Tutorial Data]]

* Another detailed training tutorial on EM Segment algorithm and Slicer3 EMSegment Template Builder module
[http://wiki.na-mic.org/Wiki/images/2/2f/AutomaticSegmentation_SoniaPujol_Munich2008.ppt Tutorial Slides] - [http://wiki.na-mic.org/Wiki/images/b/b7/AutomaticSegmentation.tar.gz Training Data]

===Quick Tour of Features and Use===
====Steps in the Workflow Wizard====
*1/9 Define Parameters Set: Select parameter set or create new parameters
*2/9 Define Hierarchy: Define a hierarchy of anatomical structures
*3/9 Assign Atlas: Assign atlases for anatomical structures
*4/9 Select Target Images: Choose the set of images that will be segmented
*5/9 Intensity Normalization: Normalize target images
*6/9 Specify Intensity Distributions: Define intensity distribution for each anatomical structure
*7/9 Edit Node-based Parameters: Specify node-based segmentation parameters
*8/9 Edit Registration Parameters: Specify atlas-to-target registration parameters
*9/9 Run Segmentation: Save work and apply EM Algorithm to segment target images

== Development ==

The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]

The module is implemented as a programmatic Slicer3 module because it
requires a large degree of interaction with the user, the data stored
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node
structure is rather complicated (for example the anatomical tissue
hierarchy and a large number of interdependent nodes) the Logic class
is solely responsible for maintaining and accessing these nodes. The
Logic class provides an API that the GUI code uses to access and
modify data. The Logic class also wraps the algorithm code itself.

===Dependencies===

Slicer3 base modules.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems.
*Atlas-to-target registration and intensity normalization are very important; it will be most effective to apply these steps using algorithms that are customized to your data. Defaults are provided but they may perform poorly for your data---this will lead to poor segmentation results.

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===

[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ Links] for the module.
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]
*API: [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentMRMLManager.html MRML Manager] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentLogic.html Module Logic] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentGUI.html Module GUI]

== More Information ==
*Some background materials: [http://wiki.na-mic.org/Wiki/index.php/EMSegmenter EMSegmenter history]
*For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]
*The old [[Modules:EM-Segmenter-Documentation:FAQ |EMSegmenter FAQ]] contains frequently asked questions about the EMSegment interfaces in Slicer3.
*There is also an old [http://www.na-mic.org/Wiki/index.php/EMSegmenter_Mini-Tutorials EMSegmenter Mini-Tutorials]

===Acknowledgment===
Funding for the EMSegmenter module was provided by NAMIC.

===References===
Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212.
[[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]

Modules:EMSegment-TemplateBuilder-3.4

2009-03-19T16:06:31Z

Yumin:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
EM Segment Template Builder

{|
|[[Image:EMSegment-Workflow.png|thumb|580px|EM Segment Workflow]]
|[[Image:EMSegment-Template.png|thumb|580px|EM Segment Template Builder GUI and EM Segment Result]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Segmentation

===Authors, Collaborators & Contact===
* Kilian Pohl: Harvard/BWH
* Brad Davis: Kitware, Inc.
* Sebastien Barre: Kitware, Inc.
* Yumin Yuan: Kitware, Inc.
* Polina Golland: MIT
* Contact: Brad Davis, brad.davis@kitware.com

===Module Description===
The EMSegment template builder module is the primary Slicer3 interface to the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. The target audience for this module is someone familiar with brain atlases and tissue labels, not a computer scientist. It allows the user to configure the algorithm---step-by-step---to a variety of imaging protocols and anatomical structures, and then apply the algorithm to segment data. Configuration settings are stored in an EMSegment parameters node in the Slicer3 MRML tree. These settings can be saved and later applied to new data via any of the EMSegment interfaces within Slicer3 or the command-line EMSegment executable.

== Usage ==

The purpose of the module is to configure the algorithm to automatically segment anatomical structures in medical images. First the user has to specify parameters defining the image protocol and the anatomical structures of interests. This process results in a template that the module uses to automatically segment large data sets. The template is composed of atlas data and a
non-trivial collection of parameters for the EMSegment algorithm.

Once the parameters are specified, the target images are segmented
using the EM Segmentation algorithm (Pohl et al.). If the results are
satisfactory, the template is saved and can be used later to segment
new images (via the GUI or batch processing). If the results are
unsatisfactory, the parameters can be modified and the segmentation
re-run.

One important aspect of the project is the workflow wizard. This
wizard simplifies the module by dividing the complicated template
specification task into a number of smaller, intuitive steps.

===Examples, Use Cases & Tutorials===

* Note use cases for which this module is especially appropriate, and/or link to examples.
* Link to examples of the module's use
* Link to any existing tutorials

===Quick Tour of Features and Use===
====Steps in the Workflow Wizard====
*1/9 Define Parameters Set: Select parameter set or create new parameters
*2/9 Define Hierarchy: Define a hierarchy of anatomical structures
*3/9 Assign Atlas: Assign atlases for anatomical structures
*4/9 Select Target Images: Choose the set of images that will be segmented
*5/9 Intensity Normalization: Normalize target images
*6/9 Specify Intensity Distributions: Define intensity distribution for each anatomical structure
*7/9 Edit Node-based Parameters: Specify node-based segmentation parameters
*8/9 Edit Registration Parameters: Specify atlas-to-target registration parameters
*9/9 Run Segmentation: Save work and apply EM Algorithm to segment target images

== Development ==

The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]

The module is implemented as a programmatic Slicer3 module because it
requires a large degree of interaction with the user, the data stored
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node
structure is rather complicated (for example the anatomical tissue
hierarchy and a large number of interdependent nodes) the Logic class
is solely responsible for maintaining and accessing these nodes. The
Logic class provides an API that the GUI code uses to access and
modify data. The Logic class also wraps the algorithm code itself.

===Dependencies===

Slicer3 base modules.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems.
*Atlas-to-target registration and intensity normalization are very important; it will be most effective to apply these steps using algorithms that are customized to your data. Defaults are provided but they may perform poorly for your data---this will lead to poor segmentation results.

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===

[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ Links] for the module.
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]
*API: [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentMRMLManager.html MRML Manager] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentLogic.html Module Logic] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentGUI.html Module GUI]

== More Information ==
*For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]
*The old [[Modules:EM-Segmenter-Documentation:FAQ |EMSegmenter FAQ]] contains frequently asked questions about the EMSegment interfaces in Slicer3.
*There is also an old [http://www.na-mic.org/Wiki/index.php/EMSegmenter_Mini-Tutorials EMSegmenter Mini-Tutorials]

===Acknowledgment===
Funding for the EMSegmenter module was provided by NAMIC.

===References===
Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212.
[[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]

Modules:EMSegment-Simple-3.4

2009-03-17T14:29:01Z

Yumin:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
EM Segment Simple
{|
|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Kilian Pohl: Harvard/BWH
* Brad Davis: Kitware, Inc.
* Sebastien Barre: Kitware, Inc.
* Yumin Yuan: Kitware, Inc.
* Polina Golland: MIT
* Contact: Brad Davis, brad.davis@kitware.com

===Module Description===
This module provide a simple and flexible parameters interface for the '''EMSegment Command-line Executable'''. The interface is simple because the number of command-line parameters is minimized, and it is flexible because any EM algorithm parameter can be modified, within the MRML scene, via the EMSegment GUI interface.

== Usage ==
Similar to the '''EMSegment Command-line Executable''', once a set of parameters for segmentation algorithm is deemed satisfactory through the process of calibrating in the '''Template Builder''' module, the user will commonly want to bypass this detailed calibration process when segmenting new images. This module provides a simple interface to specify a small number of required command-line parameters --- a MRML scene (containing algorithm parameters), a target image (or multiple target images, e.g., T1 and T2), and an output labelmap image --- , and to allow any EM algorithm parameters to be modified, within the MRML scene, via the EMSegment GUI interface.

===Examples, Use Cases & Tutorials===

* Note use cases for which this module is especially appropriate, and/or link to examples.
* Link to examples of the module's use
* Link to any existing tutorials

===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:'''
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

== Development ==
The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]

The module is implemented as a programmatic Slicer3 module because it
requires a large degree of interaction with the user, the data stored
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node
structure is rather complicated (for example the anatomical tissue
hierarchy and a large number of interdependent nodes) the Logic class
is solely responsible for maintaining and accessing these nodes. The
Logic class provides an API that the GUI code uses to access and
modify data. The Logic class also wraps the algorithm code itself.

===Dependencies===

Slicer base modules.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems.
*Atlas-to-target registration and intensity normalization are very important; it will be most effective to apply these steps using algorithms that are customized to your data. Defaults are provided but they may perform poorly for your data---this will lead to poor segmentation results.

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.

*2008: Working on a single channel T1 version of the parameter set. See [[media:EM-T1.zip|'''here''']] for the Data and such (20meg).

===Source code & documentation===

[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ Links] for the module.
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]
*API: [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentMRMLManager.html MRML Manager] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentLogic.html Module Logic] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentGUI.html Module GUI]

== More Information ==

For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]

===Acknowledgment===
Funding for the EMSegmenter module was provided by NAMIC.

===References===

Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212.
[[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]

Modules:EMSegment-Simple-3.4

2009-03-17T14:27:32Z

Yumin:

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
EM Segment Simple
{|
|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Kilian Pohl: Harvard/BWH
* Brad Davis: Kitware, Inc.
* Sebastien Barre: Kitware, Inc.
* Yumin Yuan: Kitware, Inc.
* Polina Golland: MIT
* Contact: Brad Davis, brad.davis@kitware.com

===Module Description===
This module provide a simple and flexible parameters interface for the '''EMSegment Command-line Executable'''. The interface is simple because the number of command-line parameters is minimized, and it is flexible because any EM algorithm parameter can be modified, within the MRML scene, via the EMSegment GUI interface.

== Usage ==
Similar to the '''EMSegment Command-line Executable''', once a set of parameters for segmentation algorithm is deemed satisfactory through the process of calibrating in the '''Template Builder''' module, the user will commonly want to bypass this detailed calibration process when segmenting new images. This module provides a simple interface to specify a small number of required command-line parameters --- a MRML scene (containing algorithm parameters), a target image (or multiple target images, e.g., T1 and T2), and an output labelmap image --- , and to allow any EM algorithm parameters to be modified, within the MRML scene, via the EMSegment GUI interface.

===Examples, Use Cases & Tutorials===

* Note use cases for which this module is especially appropriate, and/or link to examples.
* Link to examples of the module's use
* Link to any existing tutorials

===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:'''
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

== Development ==
The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]

The module is implemented as a programmatic Slicer3 module because it
requires a large degree of interaction with the user, the data stored
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node
structure is rather complicated (for example the anatomical tissue
hierarchy and a large number of interdependent nodes) the Logic class
is solely responsible for maintaining and accessing these nodes. The
Logic class provides an API that the GUI code uses to access and
modify data. The Logic class also wraps the algorithm code itself.

===Dependencies===

Slicer base modules.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems.
*Atlas-to-target registration and intensity normalization are very important; it will be most effective to apply these steps using algorithms that are customized to your data. Defaults are provided but they may perform poorly for your data---this will lead to poor segmentation results.

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.

*2008: Working on a single channel T1 version of the parameter set. See [[media:EM-T1.zip|'''here''']] for the Data and such (20meg).

===Source code & documentation===

[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ Links] for the module.
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]
*API: [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentMRMLManager.html MRML Manager] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentLogic.html Module Logic] | [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentGUI.html Module GUI]

== More Information ==
The [[Modules:EM-Segmenter-Documentation-3.2:FAQ |EMSegmenter FAQ]] contains frequently asked questions about the EMSegment interfaces in Slicer3.

For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]

===Acknowledgment===
Funding for the EMSegmenter module was provided by NAMIC.

===References===

Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212.
[[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]

Modules:EMSegment-TemplateBuilder-3.4

2009-03-17T13:46:29Z

2009-03-16T20:52:36Z

Yumin: /* Segmentation */

Note: This page is currently under construction

=Introduction=
[[Image:Base-Features-and-Modules.png|thumb|right|overview|[[Media:Integrating with Slicer3.ppt | Integrating with Slicer3]]]]
This page is a portal for documentation about Slicer 3.4.
For information for software developers, please go to the Developers page (see link in navigation box to the left).

=How-To Tutorials=
[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training Slicer3 tutorial page]

=Feature Request and Problem Reports=
We have an [http://www.na-mic.org/Bug/my_view_page.php issues tracker] for Slicer 3. You need to create an account for filing reports. We keep track of both feature requests and bug reports. Make sure to use the pull-down in the upper right to select Slicer 3.

=List of Modules=
==Overview==
*The documentation on this page has been created for Slicer 3.4 and discusses the features and capabilities of menu items and panels. It is intended to be used as a live reference manual. This is a wiki. You are welcome to add to the content and improve it.
*In addition to the hundereds of smaller changes and improvements to Slicer in general, there are two substantial new addtions to Slicer 3.4:
**A new infrastructure to find and add plug-ins from a repository. See [[Documentation-3.4#Modules_for_Downloading|here]] for more information.
**A new database using XNAT desktop. See [[Documentation-3.4#XNAT_Desktop|here]] for more information.

==Main GUI==
*[[Modules:MainApplicationGUI-Documentation-3.4| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.4| List of Hotkeys and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.4| How to load data]] (Steve Pieper)
*[[Modules:Saving-Documentation-3.4| Save Scene and Data Module]] (Wendy Plesniak)

==Modules==
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.4_Template|Slicer3:Module_Documentation-3.4_Template]]
*See above for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]
===Core===
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)

*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel)
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich)

*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller)
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin)

*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper)
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich)
*[[Modules:VolumeRendering-Documentation-3.4| Volume Rendering Module]] (Alex Yarmarkovich)

==Other Modules==

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.4|My Module Name With Spaces] ] (First Last Name)
===Wizards===
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta)
===Informatics Modules===
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak)
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin)
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak)
===Registration===
*Overview:
**The Register Images module is an integrated solution to all your registration needs, if you want to have a resampled volume as output. It provides access to rigid, affine and b-spline itk technologies.
**The Transforms Module allows to manually align two volumes. This can be used for initial alignment.
**Linear, affine and Deformable B-Spline modules can be used stand-alone or one after the other. They can accept transformation matrices as the start pose and produce either transforms or resampled volumes as output.
**Transformation matrices derived from these modules can be used as input for resampling other volumes (including DTI) using the Resample Volume 2 module.
*[[Modules:RegisterImages-Documentation-3.4|Register Images]] (Stephen Aylward, Ron Kikinis)
*[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek)
*[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek)
*[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen)
*[[Modules:RealignVolume-Documentation-3.4|Realign Volume]] (Nicole Aucoin)

===Segmentation===
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder)
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder)
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder)
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller)
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen)

===Statistics===
*Calculate Volume Statistics (Tri Ngo)
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper)
===DWI and Tractography===
====DWI====
*Estimation
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien von Siebenthal)
*Filter
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez)
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez, Marc Niethammer)
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja Fernandez)
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien von Siebenthal)
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien von Siebenthal)

====DTI====
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin)
*[[Modules:DTIDisplay-Documentation-3.4|Display]] (Alex Yarmakovich)
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
*Analysis
**[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
**[[Modules:ROISeeding-Documentation-3.4 | ROI Seeding]] (Raul San Jose Estepar)
**[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien von Siebenthal)
===IGT===
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda)
===Filtering===
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen)
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen)
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin)
*Arithmetic
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen)
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen)
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen)
===Surface Models===
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin)
*Grayscale Model Maker (Bill Lorensen)

*Freesurfer Surface Section Extraction (Katharina Quintus)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich)
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin)

===Batch processing===
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segementer batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian blur batch]] (Julien Jomier, Stephen Aylward)

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen)
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen)

===Work in Progress===

===Developer Tools===
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonScript-Documentation-3.4| Python Script]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonNumpyScript-Documentation-3.4| Python Numpy Script]] (Luca Antiga, Daniel Blezek)
*[[Modules:ExecutionModelTour-Documentation-3.4|Execution Model Tour]] (Daniel Blezek, Bill Lorensen)
*[[Modules:ScriptedModuleExample-Documentation-3.4| Scripted Module Example]] (Steve Pieper)

=Modules for Downloading=
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
Work is in progress to create infrastructure for searching and loading plug-in modules. See [[Slicer3:Loadable_Modules:Status_2009-01-20|here]] for more information.
*This will allow contributors and software developers to post their own Slicer plug-ins and have them compiled against the "official" versions of Slicer.
*Users can browse these contributed plug-ins and install them on their own versions of Slicer.

We are currently using NITRC as a repository for contributed modules. As a general rule, we do not test them ourselves, it is the downloaders job to ensure that they do what they want them to do.
Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 modules on NITRC.

=XNAT Desktop and FetchMI=
*Work is underway to use XNAT desktop (xnd) as a local database for Slicer. This database will exist in parallel with the other load and save mechanisms and will allow to download/upload individual files or entire scenes with all their dependent files.
*Users of Slicer will have to install xnd on their computer. Once set up, the FetchMI interface will allow users to upload and download mrml scenes with all the dependent files, or individual volumes, models, other components of slicer scenes.
*See [http://nrg.wustl.edu/xnd/download here] for a link to the download site for xnd. See [http://www.xnat.org/xnd here] for documentation on how to install XNAT desktop on your computer.
*'''On Macs and Linux you currently have to change permissions of the executable after installation.'''
*In the future (summer 2009) xnd will be able to upload and download mrml scenes to xnat enterprise.

*FetchMI is the current interface inside slicer for exploring information stored in xnd and down and upload such data.
*See [[Modules:FetchMI-Documentation-3.4|here]] for more information about FETCHMI

= Requirements for modules to be added to the release=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''' for the tasks advertised on 2-4-2009
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.4#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.4#Modules|'''here''']] to structure your page.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledgment''' tab of the module. Please see the '''Models module''' for and example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module.
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* If your module has [[Documentation-3.2|documentation in Slicer 3.2]], please copy/paste/update into the 3.4 version
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

User:Barre/TODO

2008-09-05T19:03:02Z

Yumin:

==[[2008 June Workshop Germany |Training Event in Germany]]==

Notes from a session with Ron, important items to address to improve Slicer3 usability.

# Save Data: how can one save a data file as a specific/different ITK file format. ITK uses a IO plugin framework to support new file formats: is there a way to find the list of file formats supported by ITK at run-time.
#* I (Seb) to check with Luis
#* '''[UPDATE]''' see ImageFileReader<...>::GenerateOutputInformation, BUT every IO file/reader need to expose the list of file extensions it can read and write. Luis is on it, to be added 3.8 end of July. Luis is fast, it's [http://public.kitware.com/cgi-bin/viewcvs.cgi/Code/IO/itkImageIOBase.h?root=Insight&r1=1.48&r2=1.49 in the CVS], and examplified in [http://public.kitware.com/cgi-bin/viewcvs.cgi/Testing/Code/IO/itkImageIOFileNameExtensionsTests.cxx?root=Insight&sortby=date&view=log itkImageIOFileNameExtensionsTests.cxx]
# Save Data: the "Save" dialog in general is very confusing and buggy. The "Save All" and "Save None" button are mislabelled since they don't perform any save. Saving data to a new file format requires the user to double-click in the file name and manually change the file extension (provided that this extension is known to the user). Changing the data directory does not update the data locations in the multicolumn list (it does if you change the data directory twice). Changing the scene directory has no impact on the data directory.
#* I (Seb) suggest that the "Save All/None" should be something like "Mark all for save", "Mark none for save". A button should be placed next to each data filename/location to quickly switch to a new file type (depending on what ITK can save to at run-time). The dialog is large, we have room to put a help string/label that explains a little more how the whole dialog works. Changing the data directory should update the location of each data entry in the multicolumn list correctly. A button should be added to quickly set the data directory to match the scene directory (it should not be automatic though).
#* (wjp): How about something like one of the following designs (comments/revising welcome):

[[image:SaveDesign1.png]]

[[image:SaveDesign2.png]]

The designs include the following adjustments:
* Save data options come first, scene options second
* Node type is the second column
* "Not modified" status is displayed in grey, so that "Modified" status stands out
* Format column is added, showing (optionally) the current format and an icon-button for switching (imagine clicking button, having pop-up widget for choosing among supported file formats. Once a format has been confirmed, the file name is changed to show the new file extension, and if required, "Not Modified" changes to "Modified". Should "save" also be automatically selected too? -- I think probably yes, but this may turn out to be annoying.
(SP) Yes, it would be useful to have 'Save' automatically selected after changing the file extension.
* buttons for "Check all" "Check none" are below multi-column
* Save scene checkbutton is gone -- instead user is given three options at the GUI bottom.
* Wonder if "Save Data" should be changed to "Save Data Only"?
(SP) Yes, that would make things clearer.

Icons are here, in case we want to use one of them...

[[image:FormatSelectButtonIcon1.png]]

[[image:FormatSelectButtonIcon2.png]]

Here's another stab at this widget after playing with it for awhile:
* Controls that set parameters for all datasets (check all, uncheck all, set data dir for all) are clustered together.
* User has two ways to change format easily -- using the format icon button and editing the filename.
* User has two ways to specify the save data directory (the button for all files, and individual buttons for individual datasets.)

Previously, the path name had to be hand edited, which is an error-prone exercise. The filename (and extension) were often trailing off the end of the window, so one had to click and scroll in the filename column in order to see the entire path or discover the dataset format. (Image has been updated to reflect review with Yumin and Wendy).

[[image:SaveDesign3.png]]

* '''[UPDATE]''' (Yumin)
Here is an actual screen shot of the working-copy save dialog from my machine (it does not yet have the new design for options to save locally or remotely),

[[Image:WorkCopySaveDialog.png]]

It has the following changes:
* The "Select/Save" column is moved to be the first column.
* The "File Format" column is using a dropdown list, instead of using an icon to invoke another widget. The actual displayed texts for file formats in the dropdown lists are still being worked on as we are adding necessary APIs into itkImageIO.

Below is a sketch for changes to the widget to expose functionality for saving to either local disk or remote repositories. This sketch is NOT ready to be acted upon -- just put here for discussion for now.

[[image:SaveData4.png]]

# Font Size: the font is definitely too small for the "Modules" menubutton or the filename label in any of the Red/Yellow/Green slice viewports. The "View -> Font Size" menu does not report the current font size.
#* My (Seb) opinion is to avoid hard-coding font size as much as possible, and not let the user override either font size or font family: we can not support all the possible layout combinations, or guarantee it will all fit; let's focus instead on making sure it looks nice and fit decently with the default system font size. The label in the RYG slice viewports is cropped automatically to something likely too small, and not updated later on when the slice viewport is resized/maximized: to fix.
#* Ron: Starting with the system default font is a good idea. I have encountered many situations where it is critical to be able to change the font to larger or smaller. Having a keyboard shortcut for situations where the menu is not accessible might be a good idea too: Ctrl + and ctrl - come to mind, like in firefox.
#* '''[UPDATE]''' Starting the font cleanup, will keep only the default font size, and a smaller one computed from the system default (instead of hardcoding everything), and possibility of increasing from there.
# Progress Bar: the progress bar used while loading data has been removed because it was triggering too many "update idletasks". We still need one though.
#* Steve suggests creating an OpenGL progress bar directly inside a small renderwindow. I (Seb) checked VTK's scale/slider interaction widget to see if that would do the trick. To be investigated further with the VTK's widget guru, Will.
#* '''[UPDATE]''' Actually a better starting point could be the vtkBarChartActor since each bar can be used for the multi-progress widget in KWW; Will will add an option to have it horizontal.
# Models, tree: the tree in "Models -> Hierarchy -> Model Hierarchy" may be too small for some users, as it gets more and more crowded.
#* My (Seb) opinion is that we can't have it resize automatically because who knows how tall it could be, and it would push everything down. Ron is OK to have an option to do it manually, so I plan to add two icon/buttons to increase/decrease the height (numbe of lines) of the tree, say add 15 more lines, and double the size, etc. I wish we could just "drag" the whole tree frame to a new size, like expanding a window, but that's just too hard (or impossible) to implement with this Tk widget.
#* '''[UPDATE]''' vtkKWTreeWithScrollbars has now a ResizeButtonsVisibility flag that is set for the models and MRML tree, and allow for two small resize buttons to be used to resize a tree.[[Image:KWWidgetsExpandTreeButton.png|center|thumb|250px]]
# Models, tree: the tree in "Models -> Hierarchy -> Model Hierarchy" is not as intuitive as the previous UI found in Slicer2; for each model, one could check/uncheck the visibility and change the opacity using controls placed directly next to the model's name (i.e. on the same row). The model name/label itself would use a background color matching the color used to display the model in the 3D view, a nice hint. The tree used in Slicer3 does not do nearly as much, i.e. the user has to select a node then change its visibily using a checkbutton placed in a different frame below the tree (note that the visibility and color can be changed quickly though, by using a popup menu by right-clicking on the tree leaf).
#* I (Seb) had several discussion about this item with Alex, and I'm still not sure why this can't be done technically by adding custom widgets next to the label name for each leaf in the tree, but I will have a look at it again. Given the size of the testing scene (say, 200 elements), the multicolumn widget would be too slow if each row had a label, a color button, a visibility button, etc., and the indentation would be a ugly hack. The tree widget does support custom widgets per row, but not in separate columns: they would be misaligned (either on the left or right of a leaf label).
#* '''[UPDATE]''' It seems we need the TkTreeCtrl widget which was added last year when this problem was raised already; Seb to create a C++ class around this monster library and expose only the methods we need for this very specific problem; it will take some time, since TkTreeCtrl is the most complex Tcl/Tk widget to be found in KWWidgets so far.

File:WorkCopySaveDialog.png

2008-09-05T18:57:09Z

Yumin: