https://www.slicer.org/w/api.php?action=feedcontributions&user=Davisb&feedformat=atomSlicer Wiki - User contributions [en]2024-03-28T12:44:25ZUser contributionsMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=File:EMSVisualizeTutorialInputData.png&diff=6358File:EMSVisualizeTutorialInputData.png2008-09-09T20:53:26Z<p>Davisb: </p>
<hr />
<div></div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=6225Modules:EM-Segmenter-Documentation2008-08-30T16:15:17Z<p>Davisb: /* More Information */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
EMSegmenter<br />
<br />
<gallery><br />
Image:EMSVisualizeTutorialResultsData.png|EMSegmenter Applied to MR T1 & T2 tutorial data<br />
Image:EMSegment31Structures.png|Segmentation of brain structures using EMSegmenter<br />
</gallery><br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive Module (Template Builder), CLI Module (EMSegment Simple), and Command Line Executable<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard/BWH<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
====EMSegment Workflow Module====<br />
<br />
The EMSegment worfklow module is the primary Slicer3 interface to the EMSegment algorithm. 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. <br />
<br />
A similar EMSegment module is available in Slicer2.6. The intent of<br />
this project is to implement a Slicer3 module with similar<br />
functionality while also improving the graphical user interface (GUI).<br />
While the GUI and data structure (MRML) code was completely rewritten<br />
for the Slicer3 module, the algorithm code was not modified.<br />
<br />
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<br />
non-trivial collection of parameters for the EMSegment algorithm. <br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al.). If the results are<br />
satisfactory, the template is saved and can be used later to segment<br />
new images (via the GUI or batch processing). If the results are<br />
unsatisfactory, the parameters can be modified and the segmentation<br />
re-run.<br />
<br />
One important aspect of the project is the workflow wizard. This<br />
wizard simplifies the module by dividing the complicated template<br />
specification task into a number of smaller, intuitive steps.<br />
<br />
====Steps in EMSegment Workflow====<br />
*1/9 Define Parameters Set: Select parameter set or create new parameters<br />
*2/9 Define Hierarchy: Define a hierarchy of anatomical structures<br />
*3/9 Assign Atlas: Assign atlases for anatomical structures<br />
*4/9 Select Target Images: Choose the set of images that will be segmented<br />
*5/9 Intensity Normalization: Normalize target images<br />
*6/9 Specify Intensity Distributions: Define intensity distribution for each anatomical structure<br />
*7/9 Edit Node-based Parameters: Specify node-based segmentation parameters<br />
*8/9 Edit Registration Parameters: Specify atlas-to-target registration parameters<br />
*9/9 Run Segmentation: Save work and apply EM Algorithm to segment target images<br />
<br />
====EMSegment Command-line Executable====<br />
<br />
The EMSegment command-line executable is used to simplify the processing of large collections of images. The primary function of the '''work flow''' module is to step the user through the process of calibrating, via algorithm parameters, the segmentation algorithm to a particular set of input data. However, once a successful collection of parameters is established, the user will commonly want to bypass this detailed calibration process when segmenting new images. The command-line executable provides this batch processing capability.<br />
<br />
The executable is included in the Slicer3 distribution.<br />
<br />
The interface to the executable is both simple and flexible. It is simple because the number of command-line parameters is minimized---only a MRML scene (containing algorithm parameters), a target image (or multiple target images, e.g., T1 and T2), and an output labelmap image need to be specified. It is flexible because any EM algorithm parameter can be modified, within the MRML scene, via the EMSegment GUI interface.<br />
<br />
The interface is under construction and subject to change; [[Modules:EM-Segmenter-Documentation:CommandLineInterface | here is the current version]].<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]<br />
<br />
The module is implemented as a programmatic Slicer3 module because it<br />
requires a large degree of interaction with the user, the data stored<br />
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node<br />
structure is rather complicated (for example the anatomical tissue<br />
hierarchy and a large number of interdependent nodes) the Logic class<br />
is solely responsible for maintaining and accessing these nodes. The<br />
Logic class provides an API that the GUI code uses to access and<br />
modify data. The Logic class also wraps the algorithm code itself.<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
===Usability issues===<br />
<br />
The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems. <br />
*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.<br />
<br />
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.<br />
<br />
*2008: Working on a single channel T1 version of the parameter set. See [[media:EM-T1.zip|'''here''']] for the Data and such (20meg).<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
===Priorities for Future Work===<br />
*Development<br />
**Incorporate optimized registration<br />
**Catch up on recent Slicer3 improvements/changes (how do they effect EMSegmenter?)<br />
**Bugs in Mantis: monitor, triage, fix<br />
**How to build a shape atlas: what is needed as input, how to generate the atlas<br />
**Input of weights as table instead of one by one. The current workflow is unnecessarily tedious.<br />
*Documentation<br />
**Improve help text within template builder<br />
**Expand mini-tutorial/FAQ page<br />
**Expand tutorial: single channel T1 scenario, 31 structures for single channel, dual channel<br />
**Add tutorial data sets<br />
<br />
== More Information == <br />
The [[Modules:EM-Segmenter-Documentation:FAQ |EMSegmenter FAQ]] contains frequently asked questions about the EMSegment interfaces in Slicer3.<br />
<br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
<br />
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.<br />
[[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation-3.2&diff=7459Modules:EM-Segmenter-Documentation-3.22008-08-30T16:15:17Z<p>Davisb: /* More Information */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
EMSegmenter<br />
<br />
<gallery><br />
Image:EMSVisualizeTutorialResultsData.png|EMSegmenter Applied to MR T1 & T2 tutorial data<br />
Image:EMSegment31Structures.png|Segmentation of brain structures using EMSegmenter<br />
</gallery><br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive Module (Template Builder), CLI Module (EMSegment Simple), and Command Line Executable<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard/BWH<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
====EMSegment Workflow Module====<br />
<br />
The EMSegment worfklow module is the primary Slicer3 interface to the EMSegment algorithm. 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. <br />
<br />
A similar EMSegment module is available in Slicer2.6. The intent of<br />
this project is to implement a Slicer3 module with similar<br />
functionality while also improving the graphical user interface (GUI).<br />
While the GUI and data structure (MRML) code was completely rewritten<br />
for the Slicer3 module, the algorithm code was not modified.<br />
<br />
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<br />
non-trivial collection of parameters for the EMSegment algorithm. <br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al.). If the results are<br />
satisfactory, the template is saved and can be used later to segment<br />
new images (via the GUI or batch processing). If the results are<br />
unsatisfactory, the parameters can be modified and the segmentation<br />
re-run.<br />
<br />
One important aspect of the project is the workflow wizard. This<br />
wizard simplifies the module by dividing the complicated template<br />
specification task into a number of smaller, intuitive steps.<br />
<br />
====Steps in EMSegment Workflow====<br />
*1/9 Define Parameters Set: Select parameter set or create new parameters<br />
*2/9 Define Hierarchy: Define a hierarchy of anatomical structures<br />
*3/9 Assign Atlas: Assign atlases for anatomical structures<br />
*4/9 Select Target Images: Choose the set of images that will be segmented<br />
*5/9 Intensity Normalization: Normalize target images<br />
*6/9 Specify Intensity Distributions: Define intensity distribution for each anatomical structure<br />
*7/9 Edit Node-based Parameters: Specify node-based segmentation parameters<br />
*8/9 Edit Registration Parameters: Specify atlas-to-target registration parameters<br />
*9/9 Run Segmentation: Save work and apply EM Algorithm to segment target images<br />
<br />
====EMSegment Command-line Executable====<br />
<br />
The EMSegment command-line executable is used to simplify the processing of large collections of images. The primary function of the '''work flow''' module is to step the user through the process of calibrating, via algorithm parameters, the segmentation algorithm to a particular set of input data. However, once a successful collection of parameters is established, the user will commonly want to bypass this detailed calibration process when segmenting new images. The command-line executable provides this batch processing capability.<br />
<br />
The executable is included in the Slicer3 distribution.<br />
<br />
The interface to the executable is both simple and flexible. It is simple because the number of command-line parameters is minimized---only a MRML scene (containing algorithm parameters), a target image (or multiple target images, e.g., T1 and T2), and an output labelmap image need to be specified. It is flexible because any EM algorithm parameter can be modified, within the MRML scene, via the EMSegment GUI interface.<br />
<br />
The interface is under construction and subject to change; [[Modules:EM-Segmenter-Documentation-3.2:CommandLineInterface | here is the current version]].<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]<br />
<br />
The module is implemented as a programmatic Slicer3 module because it<br />
requires a large degree of interaction with the user, the data stored<br />
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node<br />
structure is rather complicated (for example the anatomical tissue<br />
hierarchy and a large number of interdependent nodes) the Logic class<br />
is solely responsible for maintaining and accessing these nodes. The<br />
Logic class provides an API that the GUI code uses to access and<br />
modify data. The Logic class also wraps the algorithm code itself.<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
===Usability issues===<br />
<br />
The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems. <br />
*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.<br />
<br />
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.<br />
<br />
*2008: Working on a single channel T1 version of the parameter set. See [[media:EM-T1.zip|'''here''']] for the Data and such (20meg).<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
===Priorities for Future Work===<br />
*Development<br />
**Incorporate optimized registration<br />
**Catch up on recent Slicer3 improvements/changes (how do they effect EMSegmenter?)<br />
**Bugs in Mantis: monitor, triage, fix<br />
**How to build a shape atlas: what is needed as input, how to generate the atlas<br />
**Input of weights as table instead of one by one. The current workflow is unnecessarily tedious.<br />
*Documentation<br />
**Improve help text within template builder<br />
**Expand mini-tutorial/FAQ page<br />
**Expand tutorial: single channel T1 scenario, 31 structures for single channel, dual channel<br />
**Add tutorial data sets<br />
<br />
== More Information == <br />
The [[Modules:EM-Segmenter-Documentation-3.2:FAQ |EMSegmenter FAQ]] contains frequently asked questions about the EMSegment interfaces in Slicer3.<br />
<br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
<br />
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.<br />
[[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=6224Modules:EM-Segmenter-Documentation2008-08-30T16:08:24Z<p>Davisb: /* Module Name */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
EMSegmenter<br />
<br />
<gallery><br />
Image:EMSVisualizeTutorialResultsData.png|EMSegmenter Applied to MR T1 & T2 tutorial data<br />
Image:EMSegment31Structures.png|Segmentation of brain structures using EMSegmenter<br />
</gallery><br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive Module (Template Builder), CLI Module (EMSegment Simple), and Command Line Executable<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard/BWH<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
====EMSegment Workflow Module====<br />
<br />
The EMSegment worfklow module is the primary Slicer3 interface to the EMSegment algorithm. 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. <br />
<br />
A similar EMSegment module is available in Slicer2.6. The intent of<br />
this project is to implement a Slicer3 module with similar<br />
functionality while also improving the graphical user interface (GUI).<br />
While the GUI and data structure (MRML) code was completely rewritten<br />
for the Slicer3 module, the algorithm code was not modified.<br />
<br />
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<br />
non-trivial collection of parameters for the EMSegment algorithm. <br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al.). If the results are<br />
satisfactory, the template is saved and can be used later to segment<br />
new images (via the GUI or batch processing). If the results are<br />
unsatisfactory, the parameters can be modified and the segmentation<br />
re-run.<br />
<br />
One important aspect of the project is the workflow wizard. This<br />
wizard simplifies the module by dividing the complicated template<br />
specification task into a number of smaller, intuitive steps.<br />
<br />
====Steps in EMSegment Workflow====<br />
*1/9 Define Parameters Set: Select parameter set or create new parameters<br />
*2/9 Define Hierarchy: Define a hierarchy of anatomical structures<br />
*3/9 Assign Atlas: Assign atlases for anatomical structures<br />
*4/9 Select Target Images: Choose the set of images that will be segmented<br />
*5/9 Intensity Normalization: Normalize target images<br />
*6/9 Specify Intensity Distributions: Define intensity distribution for each anatomical structure<br />
*7/9 Edit Node-based Parameters: Specify node-based segmentation parameters<br />
*8/9 Edit Registration Parameters: Specify atlas-to-target registration parameters<br />
*9/9 Run Segmentation: Save work and apply EM Algorithm to segment target images<br />
<br />
====EMSegment Command-line Executable====<br />
<br />
The EMSegment command-line executable is used to simplify the processing of large collections of images. The primary function of the '''work flow''' module is to step the user through the process of calibrating, via algorithm parameters, the segmentation algorithm to a particular set of input data. However, once a successful collection of parameters is established, the user will commonly want to bypass this detailed calibration process when segmenting new images. The command-line executable provides this batch processing capability.<br />
<br />
The executable is included in the Slicer3 distribution.<br />
<br />
The interface to the executable is both simple and flexible. It is simple because the number of command-line parameters is minimized---only a MRML scene (containing algorithm parameters), a target image (or multiple target images, e.g., T1 and T2), and an output labelmap image need to be specified. It is flexible because any EM algorithm parameter can be modified, within the MRML scene, via the EMSegment GUI interface.<br />
<br />
The interface is under construction and subject to change; [[Modules:EM-Segmenter-Documentation:CommandLineInterface | here is the current version]].<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]<br />
<br />
The module is implemented as a programmatic Slicer3 module because it<br />
requires a large degree of interaction with the user, the data stored<br />
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node<br />
structure is rather complicated (for example the anatomical tissue<br />
hierarchy and a large number of interdependent nodes) the Logic class<br />
is solely responsible for maintaining and accessing these nodes. The<br />
Logic class provides an API that the GUI code uses to access and<br />
modify data. The Logic class also wraps the algorithm code itself.<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
===Usability issues===<br />
<br />
The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems. <br />
*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.<br />
<br />
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.<br />
<br />
*2008: Working on a single channel T1 version of the parameter set. See [[media:EM-T1.zip|'''here''']] for the Data and such (20meg).<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
===Priorities for Future Work===<br />
*Development<br />
**Incorporate optimized registration<br />
**Catch up on recent Slicer3 improvements/changes (how do they effect EMSegmenter?)<br />
**Bugs in Mantis: monitor, triage, fix<br />
**How to build a shape atlas: what is needed as input, how to generate the atlas<br />
**Input of weights as table instead of one by one. The current workflow is unnecessarily tedious.<br />
*Documentation<br />
**Improve help text within template builder<br />
**Expand mini-tutorial/FAQ page<br />
**Expand tutorial: single channel T1 scenario, 31 structures for single channel, dual channel<br />
**Add tutorial data sets<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
<br />
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.<br />
[[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=6064Modules:EM-Segmenter-Documentation2008-08-25T15:24:14Z<p>Davisb: /* Development */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
<gallery><br />
Image:EMSVisualizeTutorialResultsData.png|EMSegmenter Applied to MR T1 & T2 tutorial data<br />
Image:EMSegment31Structures.png|Segmentation of brain structures using EMSegmenter<br />
Image:screenshotBlank.png|Caption 3<br />
</gallery><br />
<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive Module (Template Builder), CLI Module (EMSegment Simple), and Command Line Executable<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard/BWH<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
====EMSegment Workflow Module====<br />
<br />
The EMSegment worfklow module is the primary Slicer3 interface to the EMSegment algorithm. 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. <br />
<br />
A similar EMSegment module is available in Slicer2.6. The intent of<br />
this project is to implement a Slicer3 module with similar<br />
functionality while also improving the graphical user interface (GUI).<br />
While the GUI and data structure (MRML) code was completely rewritten<br />
for the Slicer3 module, the algorithm code was not modified.<br />
<br />
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<br />
non-trivial collection of parameters for the EMSegment algorithm. <br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al.). If the results are<br />
satisfactory, the template is saved and can be used later to segment<br />
new images (via the GUI or batch processing). If the results are<br />
unsatisfactory, the parameters can be modified and the segmentation<br />
re-run.<br />
<br />
One important aspect of the project is the workflow wizard. This<br />
wizard simplifies the module by dividing the complicated template<br />
specification task into a number of smaller, intuitive steps.<br />
<br />
====Steps in EMSegment Workflow====<br />
*1/9 Define Parameters Set: Select parameter set or create new parameters<br />
*2/9 Define Hierarchy: Define a hierarchy of anatomical structures<br />
*3/9 Assign Atlas: Assign atlases for anatomical structures<br />
*4/9 Select Target Images: Choose the set of images that will be segmented<br />
*5/9 Intensity Normalization: Normalize target images<br />
*6/9 Specify Intensity Distributions: Define intensity distribution for each anatomical structure<br />
*7/9 Edit Node-based Parameters: Specify node-based segmentation parameters<br />
*8/9 Edit Registration Parameters: Specify atlas-to-target registration parameters<br />
*9/9 Run Segmentation: Save work and apply EM Algorithm to segment target images<br />
<br />
====EMSegment Command-line Executable====<br />
<br />
The EMSegment command-line executable is used to simplify the processing of large collections of images. The primary function of the '''work flow''' module is to step the user through the process of calibrating, via algorithm parameters, the segmentation algorithm to a particular set of input data. However, once a successful collection of parameters is established, the user will commonly want to bypass this detailed calibration process when segmenting new images. The command-line executable provides this batch processing capability.<br />
<br />
The executable is included in the Slicer3 distribution.<br />
<br />
The interface to the executable is both simple and flexible. It is simple because the number of command-line parameters is minimized---only a MRML scene (containing algorithm parameters), a target image (or multiple target images, e.g., T1 and T2), and an output labelmap image need to be specified. It is flexible because any EM algorithm parameter can be modified, within the MRML scene, via the EMSegment GUI interface.<br />
<br />
The interface is under construction and subject to change; [[Modules:EM-Segmenter-Documentation:CommandLineInterface | here is the current version]].<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]<br />
<br />
The module is implemented as a programmatic Slicer3 module because it<br />
requires a large degree of interaction with the user, the data stored<br />
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node<br />
structure is rather complicated (for example the anatomical tissue<br />
hierarchy and a large number of interdependent nodes) the Logic class<br />
is solely responsible for maintaining and accessing these nodes. The<br />
Logic class provides an API that the GUI code uses to access and<br />
modify data. The Logic class also wraps the algorithm code itself.<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
===Usability issues===<br />
<br />
The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems. <br />
*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.<br />
<br />
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.<br />
<br />
*2008: Working on a single channel T1 version of the parameter set. See [[media:EM-T1.zip|'''here''']] for the Data and such (20meg).<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
===Priorities for Future Work===<br />
*Development<br />
**Incorporate optimized registration<br />
**Catch up on recent Slicer3 improvements/changes (how do they effect EMSegmenter?)<br />
**Bugs in Mantis: monitor, triage, fix<br />
*Documentation<br />
**Improve help text within template builder<br />
**Expand mini-tutorial/FAQ page<br />
**Expand tutorial<br />
**Add tutorial data sets<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
<br />
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.<br />
[[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation:CommandLineInterface&diff=4974Modules:EM-Segmenter-Documentation:CommandLineInterface2008-05-28T13:43:48Z<p>Davisb: New page: USAGE: ./EMSegmentCommandLine [--processinformationaddress <std::string>] [--xml] [--echo] [--disableCompression] [--resultMRMLS...</p>
<hr />
<div>USAGE: <br />
<br />
./EMSegmentCommandLine [--processinformationaddress <std::string>]<br />
[--xml] [--echo] [--disableCompression]<br />
[--resultMRMLSceneFileName <std::string>]<br />
[--generateEmptyMRMLSceneAndQuit <std::string>]<br />
[--dontWriteResults]<br />
[--resultStandardVolumeFileName <std::string>]<br />
[--verbose] [--dontUpdateIntermediateData]<br />
[--disableMultithreading]<br />
[--parametersMRMLNodeName <std::string>]<br />
[--intermediateResultsDirectory <std::string>]<br />
[--atlasVolumeFileNames<br />
<std::vector<std::string>>] ... <br />
[--targetVolumeFileNames<br />
<std::vector<std::string>>] ... <br />
[--resultVolumeFileName <std::string>]<br />
[--mrmlSceneFileName <std::string>] [--]<br />
[--version] [-h]<br />
<br />
<br />
Where: <br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--disableCompression<br />
Don't use compression when writing result image to disk. (default: 0)<br />
<br />
--resultMRMLSceneFileName <std::string><br />
Write out the MRML scene after command line substitutions have been<br />
made.<br />
<br />
--generateEmptyMRMLSceneAndQuit <std::string><br />
Used for testing. Only write a scene with default mrml parameters.<br />
<br />
--dontWriteResults<br />
Used for testing. Don't actually write the resulting labelmap to<br />
disk. (default: 0)<br />
<br />
--resultStandardVolumeFileName <std::string><br />
Used for testing. Compare segmentation results to this image and<br />
return EXIT_FAILURE if they do not match.<br />
<br />
--verbose<br />
Enable verbose output. (default: 0)<br />
<br />
--dontUpdateIntermediateData<br />
Disable update of intermediate results. (default: 0)<br />
<br />
--disableMultithreading<br />
Disable multithreading. (default: 0)<br />
<br />
--parametersMRMLNodeName <std::string><br />
The name of the EMSegment parameters node within the active MRML<br />
scene. Leave blank for default.<br />
<br />
--intermediateResultsDirectory <std::string><br />
Directory where EMSegmenter will write intermediate data (e.g.,<br />
aligned atlas data).<br />
<br />
--atlasVolumeFileNames <std::vector<std::string>> (accepted multiple<br />
times)<br />
File names of atlas (spatial) probability maps. The number of atlas<br />
volumes must match the number specified in the parameter set. The<br />
ordering must match the ordering defined in the mrml parameters file.<br />
<br />
--targetVolumeFileNames <std::vector<std::string>> (accepted multiple<br />
times)<br />
File names of target volumes (to be segmented). The number of target<br />
images must be equal to the number of target images specified in the<br />
parameter set, and these images must be spatially aligned.<br />
<br />
--resultVolumeFileName <std::string><br />
The file name that the segmentation result volume will be written to.<br />
<br />
--mrmlSceneFileName <std::string><br />
Active MRML scene that contains EMSegment algorithm parameters.<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<br />
Description: EMSegment command-line module description and<br />
help.<br />
<br />
Author(s): Brad Davis<br />
<br />
Acknowledgements: Many people and organizations have contributed to the<br />
funding, design, and development of the EMSegment algorithm and its<br />
various implementations.</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4973Modules:EM-Segmenter-Documentation2008-05-28T13:37:55Z<p>Davisb: /* EMSegment Command-line Executable */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive Module (Template Builder), CLI Module (EMSegment Simple), and Command Line Executable<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard/BWH<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
====EMSegment Workflow Module====<br />
<br />
The EMSegment worfklow module is the primary Slicer3 interface to the EMSegment algorithm. 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. <br />
<br />
A similar EMSegment module is available in Slicer2.6. The intent of<br />
this project is to implement a Slicer3 module with similar<br />
functionality while also improving the graphical user interface (GUI).<br />
While the GUI and data structure (MRML) code was completely rewritten<br />
for the Slicer3 module, the algorithm code was not modified.<br />
<br />
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<br />
non-trivial collection of parameters for the EMSegment algorithm. <br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al.). If the results are<br />
satisfactory, the template is saved and can be used later to segment<br />
new images (via the GUI or batch processing). If the results are<br />
unsatisfactory, the parameters can be modified and the segmentation<br />
re-run.<br />
<br />
One important aspect of the project is the workflow wizard. This<br />
wizard simplifies the module by dividing the complicated template<br />
specification task into a number of smaller, intuitive steps.<br />
<br />
====Steps in EMSegment Workflow====<br />
*1/9 Define Parameters Set: Select parameter set or create new parameters<br />
*2/9 Define Hierarchy: Define a hierarchy of anatomical structures<br />
*3/9 Assign Atlas: Assign atlases for anatomical structures<br />
*4/9 Select Target Images: Choose the set of images that will be segmented<br />
*5/9 Intensity Normalization: Normalize target images<br />
*6/9 Specify Intensity Distributions: Define intensity distribution for each anatomical structure<br />
*7/9 Edit Node-based Parameters: Specify node-based segmentation parameters<br />
*8/9 Edit Registration Parameters: Specify atlas-to-target registration parameters<br />
*9/9 Run Segmentation: Save work and apply EM Algorithm to segment target images<br />
<br />
====EMSegment Command-line Executable====<br />
<br />
The EMSegment command-line executable is used to simplify the processing of large collections of images. The primary function of the '''work flow''' module is to step the user through the process of calibrating, via algorithm parameters, the segmentation algorithm to a particular set of input data. However, once a successful collection of parameters is established, the user will commonly want to bypass this detailed calibration process when segmenting new images. The command-line executable provides this batch processing capability.<br />
<br />
The executable is included in the Slicer3 distribution.<br />
<br />
The interface to the executable is both simple and flexible. It is simple because the number of command-line parameters is minimized---only a MRML scene (containing algorithm parameters), a target image (or multiple target images, e.g., T1 and T2), and an output labelmap image need to be specified. It is flexible because any EM algorithm parameter can be modified, within the MRML scene, via the EMSegment GUI interface.<br />
<br />
The interface is under construction and subject to change; [[Modules:EM-Segmenter-Documentation:CommandLineInterface | here is the current version]].<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]<br />
<br />
The module is implemented as a programmatic Slicer3 module because it<br />
requires a large degree of interaction with the user, the data stored<br />
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node<br />
structure is rather complicated (for example the anatomical tissue<br />
hierarchy and a large number of interdependent nodes) the Logic class<br />
is solely responsible for maintaining and accessing these nodes. The<br />
Logic class provides an API that the GUI code uses to access and<br />
modify data. The Logic class also wraps the algorithm code itself.<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
===Usability issues===<br />
<br />
The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems. <br />
*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.<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
<br />
K.M. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R.W. McCarley, R. Kikinis, W.E.L. Grimson, M.E. Shenton, and W.M. Wells. A hierarchical algorithm for MR brain image parcellation. IEEE Transactions on Medical Imaging, 26(9),pp 1201-1212, 2007.<br />
[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib] | [http://people.csail.mit.edu/pohl/publications/pohl-tmi-2007.pdf PDF]</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4972Modules:EM-Segmenter-Documentation2008-05-28T13:36:48Z<p>Davisb: /* Module Type & Category */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive Module (Template Builder), CLI Module (EMSegment Simple), and Command Line Executable<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard/BWH<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
====EMSegment Workflow Module====<br />
<br />
The EMSegment worfklow module is the primary Slicer3 interface to the EMSegment algorithm. 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. <br />
<br />
A similar EMSegment module is available in Slicer2.6. The intent of<br />
this project is to implement a Slicer3 module with similar<br />
functionality while also improving the graphical user interface (GUI).<br />
While the GUI and data structure (MRML) code was completely rewritten<br />
for the Slicer3 module, the algorithm code was not modified.<br />
<br />
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<br />
non-trivial collection of parameters for the EMSegment algorithm. <br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al.). If the results are<br />
satisfactory, the template is saved and can be used later to segment<br />
new images (via the GUI or batch processing). If the results are<br />
unsatisfactory, the parameters can be modified and the segmentation<br />
re-run.<br />
<br />
One important aspect of the project is the workflow wizard. This<br />
wizard simplifies the module by dividing the complicated template<br />
specification task into a number of smaller, intuitive steps.<br />
<br />
====Steps in EMSegment Workflow====<br />
*1/9 Define Parameters Set: Select parameter set or create new parameters<br />
*2/9 Define Hierarchy: Define a hierarchy of anatomical structures<br />
*3/9 Assign Atlas: Assign atlases for anatomical structures<br />
*4/9 Select Target Images: Choose the set of images that will be segmented<br />
*5/9 Intensity Normalization: Normalize target images<br />
*6/9 Specify Intensity Distributions: Define intensity distribution for each anatomical structure<br />
*7/9 Edit Node-based Parameters: Specify node-based segmentation parameters<br />
*8/9 Edit Registration Parameters: Specify atlas-to-target registration parameters<br />
*9/9 Run Segmentation: Save work and apply EM Algorithm to segment target images<br />
<br />
====EMSegment Command-line Executable====<br />
<br />
The EMSegment command-line executable is used to simplify the processing of large collections of images. The primary function of the '''work flow''' module is to step the user through the process of calibrating, via algorithm parameters, the segmentation algorithm to a particular set of input data. However, once a successful collection of parameters is established, the user will commonly want to bypass this detailed calibration process when segmenting new images. The command-line executable provides this batch processing capability.<br />
<br />
The executable is included in the Slicer3 distribution.<br />
<br />
The interface to the executable is both simple and flexible. It is simple because the number of command-line parameters is minimized---only a MRML scene (containing algorithm parameters), a target image (or multiple target images, e.g., T1 and T2), and an output labelmap image need to be specified. It is flexible because any EM algorithm parameter can be modified, within the MRML scene, via the EMSegment GUI interface.<br />
<br />
The interface is under construction and subject to change; [[Slicer3:EM:CommandLineInterface | here is the current version]].<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]<br />
<br />
The module is implemented as a programmatic Slicer3 module because it<br />
requires a large degree of interaction with the user, the data stored<br />
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node<br />
structure is rather complicated (for example the anatomical tissue<br />
hierarchy and a large number of interdependent nodes) the Logic class<br />
is solely responsible for maintaining and accessing these nodes. The<br />
Logic class provides an API that the GUI code uses to access and<br />
modify data. The Logic class also wraps the algorithm code itself.<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
===Usability issues===<br />
<br />
The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems. <br />
*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.<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
<br />
K.M. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R.W. McCarley, R. Kikinis, W.E.L. Grimson, M.E. Shenton, and W.M. Wells. A hierarchical algorithm for MR brain image parcellation. IEEE Transactions on Medical Imaging, 26(9),pp 1201-1212, 2007.<br />
[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib] | [http://people.csail.mit.edu/pohl/publications/pohl-tmi-2007.pdf PDF]</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4971Modules:EM-Segmenter-Documentation2008-05-28T13:36:12Z<p>Davisb: /* Authors, Collaborators & Contact */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard/BWH<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
====EMSegment Workflow Module====<br />
<br />
The EMSegment worfklow module is the primary Slicer3 interface to the EMSegment algorithm. 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. <br />
<br />
A similar EMSegment module is available in Slicer2.6. The intent of<br />
this project is to implement a Slicer3 module with similar<br />
functionality while also improving the graphical user interface (GUI).<br />
While the GUI and data structure (MRML) code was completely rewritten<br />
for the Slicer3 module, the algorithm code was not modified.<br />
<br />
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<br />
non-trivial collection of parameters for the EMSegment algorithm. <br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al.). If the results are<br />
satisfactory, the template is saved and can be used later to segment<br />
new images (via the GUI or batch processing). If the results are<br />
unsatisfactory, the parameters can be modified and the segmentation<br />
re-run.<br />
<br />
One important aspect of the project is the workflow wizard. This<br />
wizard simplifies the module by dividing the complicated template<br />
specification task into a number of smaller, intuitive steps.<br />
<br />
====Steps in EMSegment Workflow====<br />
*1/9 Define Parameters Set: Select parameter set or create new parameters<br />
*2/9 Define Hierarchy: Define a hierarchy of anatomical structures<br />
*3/9 Assign Atlas: Assign atlases for anatomical structures<br />
*4/9 Select Target Images: Choose the set of images that will be segmented<br />
*5/9 Intensity Normalization: Normalize target images<br />
*6/9 Specify Intensity Distributions: Define intensity distribution for each anatomical structure<br />
*7/9 Edit Node-based Parameters: Specify node-based segmentation parameters<br />
*8/9 Edit Registration Parameters: Specify atlas-to-target registration parameters<br />
*9/9 Run Segmentation: Save work and apply EM Algorithm to segment target images<br />
<br />
====EMSegment Command-line Executable====<br />
<br />
The EMSegment command-line executable is used to simplify the processing of large collections of images. The primary function of the '''work flow''' module is to step the user through the process of calibrating, via algorithm parameters, the segmentation algorithm to a particular set of input data. However, once a successful collection of parameters is established, the user will commonly want to bypass this detailed calibration process when segmenting new images. The command-line executable provides this batch processing capability.<br />
<br />
The executable is included in the Slicer3 distribution.<br />
<br />
The interface to the executable is both simple and flexible. It is simple because the number of command-line parameters is minimized---only a MRML scene (containing algorithm parameters), a target image (or multiple target images, e.g., T1 and T2), and an output labelmap image need to be specified. It is flexible because any EM algorithm parameter can be modified, within the MRML scene, via the EMSegment GUI interface.<br />
<br />
The interface is under construction and subject to change; [[Slicer3:EM:CommandLineInterface | here is the current version]].<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]<br />
<br />
The module is implemented as a programmatic Slicer3 module because it<br />
requires a large degree of interaction with the user, the data stored<br />
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node<br />
structure is rather complicated (for example the anatomical tissue<br />
hierarchy and a large number of interdependent nodes) the Logic class<br />
is solely responsible for maintaining and accessing these nodes. The<br />
Logic class provides an API that the GUI code uses to access and<br />
modify data. The Logic class also wraps the algorithm code itself.<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
===Usability issues===<br />
<br />
The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems. <br />
*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.<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
<br />
K.M. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R.W. McCarley, R. Kikinis, W.E.L. Grimson, M.E. Shenton, and W.M. Wells. A hierarchical algorithm for MR brain image parcellation. IEEE Transactions on Medical Imaging, 26(9),pp 1201-1212, 2007.<br />
[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib] | [http://people.csail.mit.edu/pohl/publications/pohl-tmi-2007.pdf PDF]</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4970Modules:EM-Segmenter-Documentation2008-05-28T13:33:20Z<p>Davisb: /* EMSegment Workflow Module */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
====EMSegment Workflow Module====<br />
<br />
The EMSegment worfklow module is the primary Slicer3 interface to the EMSegment algorithm. 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. <br />
<br />
A similar EMSegment module is available in Slicer2.6. The intent of<br />
this project is to implement a Slicer3 module with similar<br />
functionality while also improving the graphical user interface (GUI).<br />
While the GUI and data structure (MRML) code was completely rewritten<br />
for the Slicer3 module, the algorithm code was not modified.<br />
<br />
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<br />
non-trivial collection of parameters for the EMSegment algorithm. <br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al.). If the results are<br />
satisfactory, the template is saved and can be used later to segment<br />
new images (via the GUI or batch processing). If the results are<br />
unsatisfactory, the parameters can be modified and the segmentation<br />
re-run.<br />
<br />
One important aspect of the project is the workflow wizard. This<br />
wizard simplifies the module by dividing the complicated template<br />
specification task into a number of smaller, intuitive steps.<br />
<br />
====Steps in EMSegment Workflow====<br />
*1/9 Define Parameters Set: Select parameter set or create new parameters<br />
*2/9 Define Hierarchy: Define a hierarchy of anatomical structures<br />
*3/9 Assign Atlas: Assign atlases for anatomical structures<br />
*4/9 Select Target Images: Choose the set of images that will be segmented<br />
*5/9 Intensity Normalization: Normalize target images<br />
*6/9 Specify Intensity Distributions: Define intensity distribution for each anatomical structure<br />
*7/9 Edit Node-based Parameters: Specify node-based segmentation parameters<br />
*8/9 Edit Registration Parameters: Specify atlas-to-target registration parameters<br />
*9/9 Run Segmentation: Save work and apply EM Algorithm to segment target images<br />
<br />
====EMSegment Command-line Executable====<br />
<br />
The EMSegment command-line executable is used to simplify the processing of large collections of images. The primary function of the '''work flow''' module is to step the user through the process of calibrating, via algorithm parameters, the segmentation algorithm to a particular set of input data. However, once a successful collection of parameters is established, the user will commonly want to bypass this detailed calibration process when segmenting new images. The command-line executable provides this batch processing capability.<br />
<br />
The executable is included in the Slicer3 distribution.<br />
<br />
The interface to the executable is both simple and flexible. It is simple because the number of command-line parameters is minimized---only a MRML scene (containing algorithm parameters), a target image (or multiple target images, e.g., T1 and T2), and an output labelmap image need to be specified. It is flexible because any EM algorithm parameter can be modified, within the MRML scene, via the EMSegment GUI interface.<br />
<br />
The interface is under construction and subject to change; [[Slicer3:EM:CommandLineInterface | here is the current version]].<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]<br />
<br />
The module is implemented as a programmatic Slicer3 module because it<br />
requires a large degree of interaction with the user, the data stored<br />
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node<br />
structure is rather complicated (for example the anatomical tissue<br />
hierarchy and a large number of interdependent nodes) the Logic class<br />
is solely responsible for maintaining and accessing these nodes. The<br />
Logic class provides an API that the GUI code uses to access and<br />
modify data. The Logic class also wraps the algorithm code itself.<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
===Usability issues===<br />
<br />
The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems. <br />
*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.<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
<br />
K.M. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R.W. McCarley, R. Kikinis, W.E.L. Grimson, M.E. Shenton, and W.M. Wells. A hierarchical algorithm for MR brain image parcellation. IEEE Transactions on Medical Imaging, 26(9),pp 1201-1212, 2007.<br />
[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib] | [http://people.csail.mit.edu/pohl/publications/pohl-tmi-2007.pdf PDF]</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4969Modules:EM-Segmenter-Documentation2008-05-28T13:32:57Z<p>Davisb: /* EMSegment Workflow Module */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
====EMSegment Workflow Module====<br />
<br />
The EMSegment worfklow module is the primary Slicer3 interface to the EMSegment algorithm. 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. <br />
<br />
A similar EMSegment module is available in Slicer2.6. The intent of<br />
this project is to implement a Slicer3 module with similar<br />
functionality while also improving the graphical user interface (GUI).<br />
While the GUI and data structure (MRML) code was completely rewritten<br />
for the Slicer3 module, the algorithm code was not modified.<br />
<br />
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<br />
non-trivial collection of parameters for the EMSegment algorithm. <br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al.). If the results are<br />
satisfactory, the template is saved and can be used later to segment<br />
new images (via the GUI or batch processing). If the results are<br />
unsatisfactory, the parameters can be modified and the segmentation<br />
re-run.<br />
<br />
One important aspect of the project is the workflow wizard. This<br />
wizard simplifies the module by dividing the complicated template<br />
specification task into a number of smaller, intuitive steps.<br />
<br />
=====Steps in EMSegment Workflow=====<br />
*1/9 Define Parameters Set: Select parameter set or create new parameters<br />
*2/9 Define Hierarchy: Define a hierarchy of anatomical structures<br />
*3/9 Assign Atlas: Assign atlases for anatomical structures<br />
*4/9 Select Target Images: Choose the set of images that will be segmented<br />
*5/9 Intensity Normalization: Normalize target images<br />
*6/9 Specify Intensity Distributions: Define intensity distribution for each anatomical structure<br />
*7/9 Edit Node-based Parameters: Specify node-based segmentation parameters<br />
*8/9 Edit Registration Parameters: Specify atlas-to-target registration parameters<br />
*9/9 Run Segmentation: Save work and apply EM Algorithm to segment target images<br />
<br />
====EMSegment Command-line Executable====<br />
<br />
The EMSegment command-line executable is used to simplify the processing of large collections of images. The primary function of the '''work flow''' module is to step the user through the process of calibrating, via algorithm parameters, the segmentation algorithm to a particular set of input data. However, once a successful collection of parameters is established, the user will commonly want to bypass this detailed calibration process when segmenting new images. The command-line executable provides this batch processing capability.<br />
<br />
The executable is included in the Slicer3 distribution.<br />
<br />
The interface to the executable is both simple and flexible. It is simple because the number of command-line parameters is minimized---only a MRML scene (containing algorithm parameters), a target image (or multiple target images, e.g., T1 and T2), and an output labelmap image need to be specified. It is flexible because any EM algorithm parameter can be modified, within the MRML scene, via the EMSegment GUI interface.<br />
<br />
The interface is under construction and subject to change; [[Slicer3:EM:CommandLineInterface | here is the current version]].<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]<br />
<br />
The module is implemented as a programmatic Slicer3 module because it<br />
requires a large degree of interaction with the user, the data stored<br />
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node<br />
structure is rather complicated (for example the anatomical tissue<br />
hierarchy and a large number of interdependent nodes) the Logic class<br />
is solely responsible for maintaining and accessing these nodes. The<br />
Logic class provides an API that the GUI code uses to access and<br />
modify data. The Logic class also wraps the algorithm code itself.<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
===Usability issues===<br />
<br />
The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems. <br />
*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.<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
<br />
K.M. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R.W. McCarley, R. Kikinis, W.E.L. Grimson, M.E. Shenton, and W.M. Wells. A hierarchical algorithm for MR brain image parcellation. IEEE Transactions on Medical Imaging, 26(9),pp 1201-1212, 2007.<br />
[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib] | [http://people.csail.mit.edu/pohl/publications/pohl-tmi-2007.pdf PDF]</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4968Modules:EM-Segmenter-Documentation2008-05-28T13:31:49Z<p>Davisb: /* EMSegment Command-line Executable */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
====EMSegment Workflow Module====<br />
<br />
The EMSegment worfklow module is the primary Slicer3 interface to the EMSegment algorithm. 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. <br />
<br />
A similar EMSegment module is available in Slicer2.6. The intent of<br />
this project is to implement a Slicer3 module with similar<br />
functionality while also improving the graphical user interface (GUI).<br />
While the GUI and data structure (MRML) code was completely rewritten<br />
for the Slicer3 module, the algorithm code was not modified.<br />
<br />
====EMSegment Command-line Executable====<br />
<br />
The EMSegment command-line executable is used to simplify the processing of large collections of images. The primary function of the '''work flow''' module is to step the user through the process of calibrating, via algorithm parameters, the segmentation algorithm to a particular set of input data. However, once a successful collection of parameters is established, the user will commonly want to bypass this detailed calibration process when segmenting new images. The command-line executable provides this batch processing capability.<br />
<br />
The executable is included in the Slicer3 distribution.<br />
<br />
The interface to the executable is both simple and flexible. It is simple because the number of command-line parameters is minimized---only a MRML scene (containing algorithm parameters), a target image (or multiple target images, e.g., T1 and T2), and an output labelmap image need to be specified. It is flexible because any EM algorithm parameter can be modified, within the MRML scene, via the EMSegment GUI interface.<br />
<br />
The interface is under construction and subject to change; [[Slicer3:EM:CommandLineInterface | here is the current version]].<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]<br />
<br />
The module is implemented as a programmatic Slicer3 module because it<br />
requires a large degree of interaction with the user, the data stored<br />
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node<br />
structure is rather complicated (for example the anatomical tissue<br />
hierarchy and a large number of interdependent nodes) the Logic class<br />
is solely responsible for maintaining and accessing these nodes. The<br />
Logic class provides an API that the GUI code uses to access and<br />
modify data. The Logic class also wraps the algorithm code itself.<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
===Usability issues===<br />
<br />
The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems. <br />
*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.<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
<br />
K.M. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R.W. McCarley, R. Kikinis, W.E.L. Grimson, M.E. Shenton, and W.M. Wells. A hierarchical algorithm for MR brain image parcellation. IEEE Transactions on Medical Imaging, 26(9),pp 1201-1212, 2007.<br />
[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib] | [http://people.csail.mit.edu/pohl/publications/pohl-tmi-2007.pdf PDF]</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4967Modules:EM-Segmenter-Documentation2008-05-28T13:30:50Z<p>Davisb: /* Development */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
====EMSegment Workflow Module====<br />
<br />
The EMSegment worfklow module is the primary Slicer3 interface to the EMSegment algorithm. 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. <br />
<br />
A similar EMSegment module is available in Slicer2.6. The intent of<br />
this project is to implement a Slicer3 module with similar<br />
functionality while also improving the graphical user interface (GUI).<br />
While the GUI and data structure (MRML) code was completely rewritten<br />
for the Slicer3 module, the algorithm code was not modified.<br />
<br />
====EMSegment Command-line Executable====<br />
<br />
The EMSegment command-line executable is used to simplify the processing of large collections of images. The primary function of the '''work flow''' module is to step the user through the process of calibrating, via algorithm parameters, the segmentation algorithm to a particular set of input data. However, once a successful collection of parameters is established, the user will commonly want to bypass this detailed calibration process when segmenting new images. The command-line executable provides this batch processing capability.<br />
<br />
The executable is included in the Slicer3 distribution.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]<br />
<br />
The module is implemented as a programmatic Slicer3 module because it<br />
requires a large degree of interaction with the user, the data stored<br />
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node<br />
structure is rather complicated (for example the anatomical tissue<br />
hierarchy and a large number of interdependent nodes) the Logic class<br />
is solely responsible for maintaining and accessing these nodes. The<br />
Logic class provides an API that the GUI code uses to access and<br />
modify data. The Logic class also wraps the algorithm code itself.<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
===Usability issues===<br />
<br />
The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems. <br />
*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.<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
<br />
K.M. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R.W. McCarley, R. Kikinis, W.E.L. Grimson, M.E. Shenton, and W.M. Wells. A hierarchical algorithm for MR brain image parcellation. IEEE Transactions on Medical Imaging, 26(9),pp 1201-1212, 2007.<br />
[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib] | [http://people.csail.mit.edu/pohl/publications/pohl-tmi-2007.pdf PDF]</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4966Modules:EM-Segmenter-Documentation2008-05-28T13:29:40Z<p>Davisb: /* Module Description */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
====EMSegment Workflow Module====<br />
<br />
The EMSegment worfklow module is the primary Slicer3 interface to the EMSegment algorithm. 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. <br />
<br />
A similar EMSegment module is available in Slicer2.6. The intent of<br />
this project is to implement a Slicer3 module with similar<br />
functionality while also improving the graphical user interface (GUI).<br />
While the GUI and data structure (MRML) code was completely rewritten<br />
for the Slicer3 module, the algorithm code was not modified.<br />
<br />
====EMSegment Command-line Executable====<br />
<br />
The EMSegment command-line executable is used to simplify the processing of large collections of images. The primary function of the '''work flow''' module is to step the user through the process of calibrating, via algorithm parameters, the segmentation algorithm to a particular set of input data. However, once a successful collection of parameters is established, the user will commonly want to bypass this detailed calibration process when segmenting new images. The command-line executable provides this batch processing capability.<br />
<br />
The executable is included in the Slicer3 distribution.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
===Usability issues===<br />
<br />
The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems. <br />
*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.<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
<br />
K.M. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R.W. McCarley, R. Kikinis, W.E.L. Grimson, M.E. Shenton, and W.M. Wells. A hierarchical algorithm for MR brain image parcellation. IEEE Transactions on Medical Imaging, 26(9),pp 1201-1212, 2007.<br />
[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib] | [http://people.csail.mit.edu/pohl/publications/pohl-tmi-2007.pdf PDF]</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4965Modules:EM-Segmenter-Documentation2008-05-28T13:28:21Z<p>Davisb: /* Development */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides.]]<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
===Usability issues===<br />
<br />
The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems. <br />
*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.<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
<br />
K.M. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R.W. McCarley, R. Kikinis, W.E.L. Grimson, M.E. Shenton, and W.M. Wells. A hierarchical algorithm for MR brain image parcellation. IEEE Transactions on Medical Imaging, 26(9),pp 1201-1212, 2007.<br />
[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib] | [http://people.csail.mit.edu/pohl/publications/pohl-tmi-2007.pdf PDF]</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4964Modules:EM-Segmenter-Documentation2008-05-28T13:28:08Z<p>Davisb: /* Development */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
The overall design of the EMSegmenter module is described in [[Media:EMSegTutorial-AHM2008.ppt | these slides]]<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
===Usability issues===<br />
<br />
The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems. <br />
*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.<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
<br />
K.M. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R.W. McCarley, R. Kikinis, W.E.L. Grimson, M.E. Shenton, and W.M. Wells. A hierarchical algorithm for MR brain image parcellation. IEEE Transactions on Medical Imaging, 26(9),pp 1201-1212, 2007.<br />
[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib] | [http://people.csail.mit.edu/pohl/publications/pohl-tmi-2007.pdf PDF]</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4963Modules:EM-Segmenter-Documentation2008-05-28T13:25:24Z<p>Davisb: /* Usability issues */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
<br />
===Usability issues===<br />
<br />
The EMSegmenter can be adapted to many segmentation problems. However, there is no "default" set of parameters that will work for all segmentation problems. <br />
*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.<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
<br />
K.M. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R.W. McCarley, R. Kikinis, W.E.L. Grimson, M.E. Shenton, and W.M. Wells. A hierarchical algorithm for MR brain image parcellation. IEEE Transactions on Medical Imaging, 26(9),pp 1201-1212, 2007.<br />
[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib] | [http://people.csail.mit.edu/pohl/publications/pohl-tmi-2007.pdf PDF]</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4962Modules:EM-Segmenter-Documentation2008-05-28T13:21:55Z<p>Davisb: /* References */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
<br />
K.M. Pohl, S. Bouix, M. Nakamura, T. Rohlfing, R.W. McCarley, R. Kikinis, W.E.L. Grimson, M.E. Shenton, and W.M. Wells. A hierarchical algorithm for MR brain image parcellation. IEEE Transactions on Medical Imaging, 26(9),pp 1201-1212, 2007.<br />
[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib] | [http://people.csail.mit.edu/pohl/publications/pohl-tmi-2007.pdf PDF]</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4961Modules:EM-Segmenter-Documentation2008-05-28T13:19:33Z<p>Davisb: /* Source code & documentation */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
Kilian TMI Paper</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4960Modules:EM-Segmenter-Documentation2008-05-28T13:18:58Z<p>Davisb: /* Source code & documentation */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*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]<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
Kilian TMI Paper</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4959Modules:EM-Segmenter-Documentation2008-05-28T12:57:31Z<p>Davisb: /* Source code & documentation */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegmenter Code]<br />
*API: [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkEMSegmentLogic.html Module Logic]<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
Kilian TMI Paper</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4958Modules:EM-Segmenter-Documentation2008-05-28T12:55:45Z<p>Davisb: /* Source code & documentation */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ links] for your module.<br />
<br />
[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
Kilian TMI Paper</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4957Modules:EM-Segmenter-Documentation2008-05-28T12:54:16Z<p>Davisb: /* More Information */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.<br />
<br />
[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.<br />
<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
Kilian TMI Paper</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4956Modules:EM-Segmenter-Documentation2008-05-28T12:53:43Z<p>Davisb: /* References */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.<br />
<br />
[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.<br />
<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
Kilian TMI Paper</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4955Modules:EM-Segmenter-Documentation2008-05-28T12:53:02Z<p>Davisb: /* Acknowledgment */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.<br />
<br />
[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.<br />
<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see here]]<br />
<br />
===Acknowledgment===<br />
Funding for the EMSegmenter module was provided by NAMIC.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4954Modules:EM-Segmenter-Documentation2008-05-28T12:51:53Z<p>Davisb: /* Dependencies */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
Slicer base modules.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.<br />
<br />
[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.<br />
<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see here]]<br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4953Modules:EM-Segmenter-Documentation2008-05-28T12:50:03Z<p>Davisb: /* Module Description */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.<br />
<br />
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.<br />
<br />
[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.<br />
<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see here]]<br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4952Modules:EM-Segmenter-Documentation2008-05-28T12:49:24Z<p>Davisb: /* Authors, Collaborators & Contact */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Kilian Pohl: Harvard<br />
* Brad Davis: Kitware, Inc.<br />
* Sebastien Barre: Kitware, Inc.<br />
* Yumin Yuan: Kitware, Inc.<br />
* Polina Golland: MIT<br />
* Contact: Brad Davis, brad.davis@kitware.com<br />
<br />
===Module Description===<br />
Overview of what the module does goes here.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.<br />
<br />
[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.<br />
<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see here]]<br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4951Modules:EM-Segmenter-Documentation2008-05-28T12:47:43Z<p>Davisb: /* Module Type & Category */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive (Template Builder) and CLI (EMSegment Simple)<br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author1: Affiliation & logo, if desired<br />
* Contributor1: Affiliation & logo, if desired<br />
* Contributor2: Affiliation & logo, if desired<br />
* Contact: name, email<br />
<br />
===Module Description===<br />
Overview of what the module does goes here.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.<br />
<br />
[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.<br />
<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see here]]<br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Davisbhttps://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation&diff=4950Modules:EM-Segmenter-Documentation2008-05-28T12:47:03Z<p>Davisb: /* Module Name */</p>
<hr />
<div>[[Documentation|Return to Slicer Documentation]]<br />
__NOTOC__<br />
===Module Name===<br />
MyModule<br />
<br />
{|<br />
|[[Image:EMSVisualizeTutorialResultsData.png|thumb|280px|EMSegmenter Applied to MR T1 & T2 tutorial data]]<br />
|[[Image:EMSegment31Structures.png|thumb|280px|Segmentation of brain structures using EMSegmenter]]<br />
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]<br />
|}<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive or CLI<br />
<br />
Category: Base or (Filtering, Registration, ''etc.'')<br />
<br />
===Authors, Collaborators & Contact===<br />
* Author1: Affiliation & logo, if desired<br />
* Contributor1: Affiliation & logo, if desired<br />
* Contributor2: Affiliation & logo, if desired<br />
* Contact: name, email<br />
<br />
===Module Description===<br />
Overview of what the module does goes here.<br />
<br />
== Usage ==<br />
<br />
===Examples, Use Cases & Tutorials===<br />
<br />
* Note use cases for which this module is especially appropriate, and/or link to examples.<br />
* Link to examples of the module's use<br />
* Link to any existing tutorials<br />
<br />
===Quick Tour of Features and Use===<br />
List all the panels in your interface, their features, what they mean, and how to use them. For instance:<br />
<br />
* '''Input panel:'''<br />
* '''Parameters panel:'''<br />
* '''Output panel:'''<br />
* '''Viewing panel:'''<br />
<br />
== Development ==<br />
<br />
===Dependencies===<br />
<br />
Other modules or packages that are required for this module's use.<br />
<br />
===Known bugs===<br />
<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. <br />
<br />
<br />
<br />
===Usability issues===<br />
<br />
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.<br />
<br />
===Source code & documentation===<br />
<br />
Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.<br />
<br />
[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.<br />
<br />
<br />
== More Information == <br />
For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see here]]<br />
<br />
===Acknowledgment===<br />
Include funding and other support here.<br />
<br />
===References===<br />
Publications related to this module go here. Links to pdfs would be useful.</div>Davisbhttps://www.slicer.org/w/index.php?title=Announcements:Slicer3.2&diff=4949Announcements:Slicer3.22008-05-28T12:43:20Z<p>Davisb: </p>
<hr />
<div>=Slicer 3.2=<br />
{| border="00" cell padding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
<big> '''Slicer 3.2'''</big>, a major release of the Slicer software platform, is scheduled for release on Friday, May 30, 2008. The new release contains hundreds of changes to the software. Highlights include:<br />
<br />
* Improved Multi-platform support and availability of pre-compiled binaries for Windows, Mac OS X, and Linux<br />
* New ways to display, interact and record complex visualizations of cross-sectional and deried data<br />
* Advanced data fusion and registration capabilities<br />
* Segmentation tools<br />
* Support for complex data such as DTI<br />
* Interfaces to informatics frameworks<br />
<br />
[http://www.slicer.org/pages/Downloads Click here to download] different versions of Slicer3 and find pointers to the source code, mailing lists and bug tracker. Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer3 are not fully tested.<br />
<br />
| style="background: #C3D1C3" align="center"| [[Modules:VolumeRendering-Documentation|Integrated Volume Rendering]]: <br>View of the [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=1266 abdominal atlas]<br>Bone and large vessels are volume rendered.<br />
|-<br />
| style="background: #ebeced"|[[Image:VolRend2.png|center|350px|Example of Volume Rendering]] <br />
|}<br />
<br />
=Overview=<br />
<gallery caption="Slicer v3.2 - New and Improved Feature Highlights" widths="250px" heights="150px" perrow="4"><br />
Image:ComplexVis.png|Complex Visualization Capabilities: Combining cross-sections and 3D surface models tumor, brain morphology, MR angiogram, fMRI and DTI)<br />
Image:VolRend.png|Volume Rendering: [[Modules:VolumeRendering-Documentation|Fully integrated volume rendering]] with cropping for easy exploration of volumetric data<br />
Image:ImplicitPlane.png|Implicit Slice Widget: An interactive tool for specifying oblique views (part of the [http://www.vtk.org/Wiki/VTK_Widget_Examples VTK widget family]).<br />
Image:LightBox.png|[[Slicer3:Tools_for_Radiologists|The Lightbox]]: Functionality for displaying cross-sectional data in columns and rows.<br />
Image:Editor-v3-2.png|[[Modules:Editor-Documentation|Interactive Editor:]] This new module allows interactive segmentation with robust 2D and 3D algorithms<br />
Image:IO.png|IO: [[Documentation|Improved IO capabilities]] include support for DICOM, NRRD, NIFTI, Tiff, JPG, Freesurfer, FITS and a number of other formats<br />
Image:Line-glyph-tracts.jpg|Glyphs on tracts:<br>[[Modules:DTMRI-Documentation|New Diffusion Imaging infrastructure]] includes<br>dicom import<br>gradient editor<br>visualiztion<br />
Image:DataLoadingStartPlan.png|[[Slicer3:Remote_Data_Handling|Remote Data Handling]] allows uploads and downloads from image informatics frameworks such as BIRN, and XNAT<br />
Image:Slicer_IGTL_PartialImage.png|[http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] interfaces to devices such as scanners, trackers, and robots<br />
Image:DataFusion.png|Result of combining affine and b-Spline registration<br />
Image:EMSVisualizeTutorialResultsData.png|[[Modules:EM-Segmenter-Documentation|EM Segmenter:]] A configurable image segmentation tool that uses intensity distributions along with atlas information <br />
</gallery><br />
*[[Slicer3:Loadable_Modules|Loadable Modules]]<br />
*EM segementer<br />
*Scenesnapshots</div>Davisbhttps://www.slicer.org/w/index.php?title=Announcements:Slicer3.2&diff=4948Announcements:Slicer3.22008-05-28T12:41:40Z<p>Davisb: </p>
<hr />
<div>=Slicer 3.2=<br />
{| border="00" cell padding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
<big> '''Slicer 3.2'''</big>, a major release of the Slicer software platform, is scheduled for release on Friday, May 30, 2008. The new release contains hundreds of changes to the software. Highlights include:<br />
<br />
* Improved Multi-platform support and availability of pre-compiled binaries for Windows, Mac OS X, and Linux<br />
* New ways to display, interact and record complex visualizations of cross-sectional and deried data<br />
* Advanced data fusion and registration capabilities<br />
* Segmentation tools<br />
* Support for complex data such as DTI<br />
* Interfaces to informatics frameworks<br />
<br />
[http://www.slicer.org/pages/Downloads Click here to download] different versions of Slicer3 and find pointers to the source code, mailing lists and bug tracker. Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer3 are not fully tested.<br />
<br />
| style="background: #C3D1C3" align="center"| [[Modules:VolumeRendering-Documentation|Integrated Volume Rendering]]: <br>View of the [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=1266 abdominal atlas]<br>Bone and large vessels are volume rendered.<br />
|-<br />
| style="background: #ebeced"|[[Image:VolRend2.png|center|350px|Example of Volume Rendering]] <br />
|}<br />
<br />
=Overview=<br />
<gallery caption="Slicer v3.2 - New and Improved Feature Highlights" widths="250px" heights="150px" perrow="4"><br />
Image:ComplexVis.png|Complex Visualization Capabilities: Combining cross-sections and 3D surface models tumor, brain morphology, MR angiogram, fMRI and DTI)<br />
Image:VolRend.png|Volume Rendering: [[Modules:VolumeRendering-Documentation|Fully integrated volume rendering]] with cropping for easy exploration of volumetric data<br />
Image:ImplicitPlane.png|Implicit Slice Widget: An interactive tool for specifying oblique views (part of the [http://www.vtk.org/Wiki/VTK_Widget_Examples VTK widget family]).<br />
Image:LightBox.png|[[Slicer3:Tools_for_Radiologists|The Lightbox]]: Functionality for displaying cross-sectional data in columns and rows.<br />
Image:Editor-v3-2.png|[[Modules:Editor-Documentation|Interactive Editor:]] This new module allows interactive segmentation with robust 2D and 3D algorithms<br />
Image:IO.png|IO: [[Documentation|Improved IO capabilities]] include support for DICOM, NRRD, NIFTI, Tiff, JPG, Freesurfer, FITS and a number of other formats<br />
Image:Line-glyph-tracts.jpg|Glyphs on tracts:<br>[[Modules:DTMRI-Documentation|New Diffusion Imaging infrastructure]] includes<br>dicom import<br>gradient editor<br>visualiztion<br />
Image:DataLoadingStartPlan.png|[[Slicer3:Remote_Data_Handling|Remote Data Handling]] allows uploads and downloads from image informatics frameworks such as BIRN, and XNAT<br />
Image:Slicer_IGTL_PartialImage.png|[http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] interfaces to devices such as scanners, trackers, and robots<br />
Image:DataFusion.png|Result of combining affine and b-Spline registration<br />
Image:EMSVisualizeTutorialResultsData.png|EM Segmenter: A configurable image segmentation tool that uses intensity distributions along with atlas information <br />
</gallery><br />
*[[Slicer3:Loadable_Modules|Loadable Modules]]<br />
*EM segementer<br />
*Scenesnapshots</div>Davisbhttps://www.slicer.org/w/index.php?title=File:EMSVisualizeTutorialResultsData.png&diff=4947File:EMSVisualizeTutorialResultsData.png2008-05-28T12:40:02Z<p>Davisb: </p>
<hr />
<div></div>Davisbhttps://www.slicer.org/w/index.php?title=Announcements:Slicer3.2&diff=4946Announcements:Slicer3.22008-05-28T12:38:07Z<p>Davisb: </p>
<hr />
<div>=Slicer 3.2=<br />
{| border="00" cell padding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
<big> '''Slicer 3.2'''</big>, a major release of the Slicer software platform, is scheduled for release on Friday, May 30, 2008. The new release contains hundreds of changes to the software. Highlights include:<br />
<br />
* Improved Multi-platform support and availability of pre-compiled binaries for Windows, Mac OS X, and Linux<br />
* New ways to display, interact and record complex visualizations of cross-sectional and deried data<br />
* Advanced data fusion and registration capabilities<br />
* Segmentation tools<br />
* Support for complex data such as DTI<br />
* Interfaces to informatics frameworks<br />
<br />
[http://www.slicer.org/pages/Downloads Click here to download] different versions of Slicer3 and find pointers to the source code, mailing lists and bug tracker. Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer3 are not fully tested.<br />
<br />
| style="background: #C3D1C3" align="center"| [[Modules:VolumeRendering-Documentation|Integrated Volume Rendering]]: <br>View of the [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=1266 abdominal atlas]<br>Bone and large vessels are volume rendered.<br />
|-<br />
| style="background: #ebeced"|[[Image:VolRend2.png|center|350px|Example of Volume Rendering]] <br />
|}<br />
<br />
=Overview=<br />
<gallery caption="Slicer v3.2 - New and Improved Feature Highlights" widths="250px" heights="150px" perrow="4"><br />
Image:ComplexVis.png|Complex Visualization Capabilities: Combining cross-sections and 3D surface models tumor, brain morphology, MR angiogram, fMRI and DTI)<br />
Image:VolRend.png|Volume Rendering: [[Modules:VolumeRendering-Documentation|Fully integrated volume rendering]] with cropping for easy exploration of volumetric data<br />
Image:ImplicitPlane.png|Implicit Slice Widget: An interactive tool for specifying oblique views (part of the [http://www.vtk.org/Wiki/VTK_Widget_Examples VTK widget family]).<br />
Image:LightBox.png|[[Slicer3:Tools_for_Radiologists|The Lightbox]]: Functionality for displaying cross-sectional data in columns and rows.<br />
Image:Editor-v3-2.png|[[Modules:Editor-Documentation|Interactive Editor:]] This new module allows interactive segmentation with robust 2D and 3D algorithms<br />
Image:IO.png|IO: [[Documentation|Improved IO capabilities]] include support for DICOM, NRRD, NIFTI, Tiff, JPG, Freesurfer, FITS and a number of other formats<br />
Image:Line-glyph-tracts.jpg|Glyphs on tracts:<br>[[Modules:DTMRI-Documentation|New Diffusion Imaging infrastructure]] includes<br>dicom import<br>gradient editor<br>visualiztion<br />
Image:DataLoadingStartPlan.png|[[Slicer3:Remote_Data_Handling|Remote Data Handling]] allows uploads and downloads from image informatics frameworks such as BIRN, and XNAT<br />
Image:Slicer_IGTL_PartialImage.png|[http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] interfaces to devices such as scanners, trackers, and robots<br />
Image:DataFusion.png|Result of combining affine and b-Spline registration<br />
Image:EMSegmenterTutorialResults.png|EM Segmenter: A configurable image segmentation tool that uses intensity distributions along with atlas information <br />
</gallery><br />
*[[Slicer3:Loadable_Modules|Loadable Modules]]<br />
*EM segementer<br />
*Scenesnapshots</div>Davisbhttps://www.slicer.org/w/index.php?title=Announcements:Slicer3.2&diff=4945Announcements:Slicer3.22008-05-28T12:36:27Z<p>Davisb: </p>
<hr />
<div>=Slicer 3.2=<br />
{| border="00" cell padding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
<big> '''Slicer 3.2'''</big>, a major release of the Slicer software platform, is scheduled for release on Friday, May 30, 2008. The new release contains hundreds of changes to the software. Highlights include:<br />
<br />
* Improved Multi-platform support and availability of pre-compiled binaries for Windows, Mac OS X, and Linux<br />
* New ways to display, interact and record complex visualizations of cross-sectional and deried data<br />
* Advanced data fusion and registration capabilities<br />
* Segmentation tools<br />
* Support for complex data such as DTI<br />
* Interfaces to informatics frameworks<br />
<br />
[http://www.slicer.org/pages/Downloads Click here to download] different versions of Slicer3 and find pointers to the source code, mailing lists and bug tracker. Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer3 are not fully tested.<br />
<br />
| style="background: #C3D1C3" align="center"| [[Modules:VolumeRendering-Documentation|Integrated Volume Rendering]]: <br>View of the [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=1266 abdominal atlas]<br>Bone and large vessels are volume rendered.<br />
|-<br />
| style="background: #ebeced"|[[Image:VolRend2.png|center|350px|Example of Volume Rendering]] <br />
|}<br />
<br />
=Overview=<br />
<gallery caption="Slicer v3.2 - New and Improved Feature Highlights" widths="250px" heights="150px" perrow="4"><br />
Image:ComplexVis.png|Complex Visualization Capabilities: Combining cross-sections and 3D surface models tumor, brain morphology, MR angiogram, fMRI and DTI)<br />
Image:VolRend.png|Volume Rendering: [[Modules:VolumeRendering-Documentation|Fully integrated volume rendering]] with cropping for easy exploration of volumetric data<br />
Image:ImplicitPlane.png|Implicit Slice Widget: An interactive tool for specifying oblique views (part of the [http://www.vtk.org/Wiki/VTK_Widget_Examples VTK widget family]).<br />
Image:LightBox.png|[[Slicer3:Tools_for_Radiologists|The Lightbox]]: Functionality for displaying cross-sectional data in columns and rows.<br />
Image:Editor-v3-2.png|[[Modules:Editor-Documentation|Interactive Editor:]] This new module allows interactive segmentation with robust 2D and 3D algorithms<br />
Image:IO.png|IO: [[Documentation|Improved IO capabilities]] include support for DICOM, NRRD, NIFTI, Tiff, JPG, Freesurfer, FITS and a number of other formats<br />
Image:Line-glyph-tracts.jpg|Glyphs on tracts:<br>[[Modules:DTMRI-Documentation|New Diffusion Imaging infrastructure]] includes<br>dicom import<br>gradient editor<br>visualiztion<br />
Image:DataLoadingStartPlan.png|[[Slicer3:Remote_Data_Handling|Remote Data Handling]] allows uploads and downloads from image informatics frameworks such as BIRN, and XNAT<br />
Image:Slicer_IGTL_PartialImage.png|[http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] interfaces to devices such as scanners, trackers, and robots<br />
Image:DataFusion.png|Result of combining affine and b-Spline registration<br />
Image:EMSegmenter.png|EM Segmenter: A configurable image segmentation tool that uses intensity distributions along with atlas information <br />
</gallery><br />
*[[Slicer3:Loadable_Modules|Loadable Modules]]<br />
*EM segementer<br />
*Scenesnapshots</div>Davisbhttps://www.slicer.org/w/index.php?title=Announcements:Slicer3.2&diff=4944Announcements:Slicer3.22008-05-28T12:32:31Z<p>Davisb: </p>
<hr />
<div>=Slicer 3.2=<br />
{| border="00" cell padding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
<big> '''Slicer 3.2'''</big>, a major release of the Slicer software platform, is scheduled for release on Friday, May 30, 2008. The new release contains hundreds of changes to the software. Highlights include:<br />
<br />
* Improved Multi-platform support and availability of pre-compiled binaries for Windows, Mac OS X, and Linux<br />
* New ways to display, interact and record complex visualizations of cross-sectional and deried data<br />
* Advanced data fusion and registration capabilities<br />
* Segmentation tools<br />
* Support for complex data such as DTI<br />
* Interfaces to informatics frameworks<br />
<br />
[http://www.slicer.org/pages/Downloads Click here to download] different versions of Slicer3 and find pointers to the source code, mailing lists and bug tracker. Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer3 are not fully tested.<br />
<br />
| style="background: #C3D1C3" align="center"| [[Modules:VolumeRendering-Documentation|Integrated Volume Rendering]]: <br>View of the [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=1266 abdominal atlas]<br>Bone and large vessels are volume rendered.<br />
|-<br />
| style="background: #ebeced"|[[Image:VolRend2.png|center|350px|Example of Volume Rendering]] <br />
|}<br />
<br />
=Overview=<br />
<gallery caption="Slicer v3.2 - New and Improved Feature Highlights" widths="250px" heights="150px" perrow="4"><br />
Image:ComplexVis.png|Complex Visualization Capabilities: Combining cross-sections and 3D surface models tumor, brain morphology, MR angiogram, fMRI and DTI)<br />
Image:VolRend.png|Volume Rendering: [[Modules:VolumeRendering-Documentation|Fully integrated volume rendering]] with cropping for easy exploration of volumetric data<br />
Image:ImplicitPlane.png|Implicit Slice Widget: An interactive tool for specifying oblique views (part of the [http://www.vtk.org/Wiki/VTK_Widget_Examples VTK widget family]).<br />
Image:LightBox.png|[[Slicer3:Tools_for_Radiologists|The Lightbox]]: Functionality for displaying cross-sectional data in columns and rows.<br />
Image:Editor-v3-2.png|[[Modules:Editor-Documentation|Interactive Editor:]] This new module allows interactive segmentation with robust 2D and 3D algorithms<br />
Image:IO.png|IO: [[Documentation|Improved IO capabilities]] include support for DICOM, NRRD, NIFTI, Tiff, JPG, Freesurfer, FITS and a number of other formats<br />
Image:Line-glyph-tracts.jpg|Glyphs on tracts:<br>[[Modules:DTMRI-Documentation|New Diffusion Imaging infrastructure]] includes<br>dicom import<br>gradient editor<br>visualiztion<br />
Image:DataLoadingStartPlan.png|[[Slicer3:Remote_Data_Handling|Remote Data Handling]] allows uploads and downloads from image informatics frameworks such as BIRN, and XNAT<br />
Image:Slicer_IGTL_PartialImage.png|[http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] interfaces to devices such as scanners, trackers, and robots<br />
Image:DataFusion.png|Result of combining affine and b-Spline registration<br />
Image:EMSegmenter.png|EM Segmenter: An image segmentation tool that uses intensity distributions along with atlas information<br />
</gallery><br />
*[[Slicer3:Loadable_Modules|Loadable Modules]]<br />
*EM segementer<br />
*Scenesnapshots</div>Davisbhttps://www.slicer.org/w/index.php?title=Announcements:Slicer3.2&diff=4943Announcements:Slicer3.22008-05-28T12:32:00Z<p>Davisb: </p>
<hr />
<div>=Slicer 3.2=<br />
{| border="00" cell padding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
<big> '''Slicer 3.2'''</big>, a major release of the Slicer software platform, is scheduled for release on Friday, May 30, 2008. The new release contains hundreds of changes to the software. Highlights include:<br />
<br />
* Improved Multi-platform support and availability of pre-compiled binaries for Windows, Mac OS X, and Linux<br />
* New ways to display, interact and record complex visualizations of cross-sectional and deried data<br />
* Advanced data fusion and registration capabilities<br />
* Segmentation tools<br />
* Support for complex data such as DTI<br />
* Interfaces to informatics frameworks<br />
<br />
[http://www.slicer.org/pages/Downloads Click here to download] different versions of Slicer3 and find pointers to the source code, mailing lists and bug tracker. Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer3 are not fully tested.<br />
<br />
| style="background: #C3D1C3" align="center"| [[Modules:VolumeRendering-Documentation|Integrated Volume Rendering]]: <br>View of the [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=1266 abdominal atlas]<br>Bone and large vessels are volume rendered.<br />
|-<br />
| style="background: #ebeced"|[[Image:VolRend2.png|center|350px|Example of Volume Rendering]] <br />
|}<br />
<br />
=Overview=<br />
<gallery caption="Slicer v3.2 - New and Improved Feature Highlights" widths="250px" heights="150px" perrow="4"><br />
Image:ComplexVis.png|Complex Visualization Capabilities: Combining cross-sections and 3D surface models tumor, brain morphology, MR angiogram, fMRI and DTI)<br />
Image:VolRend.png|Volume Rendering: [[Modules:VolumeRendering-Documentation|Fully integrated volume rendering]] with cropping for easy exploration of volumetric data<br />
Image:ImplicitPlane.png|Implicit Slice Widget: An interactive tool for specifying oblique views (part of the [http://www.vtk.org/Wiki/VTK_Widget_Examples VTK widget family]).<br />
Image:LightBox.png|[[Slicer3:Tools_for_Radiologists|The Lightbox]]: Functionality for displaying cross-sectional data in columns and rows.<br />
Image:Editor-v3-2.png|[[Modules:Editor-Documentation|Interactive Editor:]] This new module allows interactive segmentation with robust 2D and 3D algorithms<br />
Image:IO.png|IO: [[Documentation|Improved IO capabilities]] include support for DICOM, NRRD, NIFTI, Tiff, JPG, Freesurfer, FITS and a number of other formats<br />
Image:Line-glyph-tracts.jpg|Glyphs on tracts:<br>[[Modules:DTMRI-Documentation|New Diffusion Imaging infrastructure]] includes<br>dicom import<br>gradient editor<br>visualiztion<br />
Image:DataLoadingStartPlan.png|[[Slicer3:Remote_Data_Handling|Remote Data Handling]] allows uploads and downloads from image informatics frameworks such as BIRN, and XNAT<br />
Image:Slicer_IGTL_PartialImage.png|[http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] interfaces to devices such as scanners, trackers, and robots<br />
Image:DataFusion.png|Result of combining affine and b-Spline registration<br />
</gallery><br />
Image:EMSegmenter.png|EM Segmenter: An image segmentation tool that uses intensity distributions along with atlas information<br />
</gallery><br />
*[[Slicer3:Loadable_Modules|Loadable Modules]]<br />
*EM segementer<br />
*Scenesnapshots</div>Davisb