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| − | =Project Summary=
| + | <big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [https://www.slicer.org/wiki/Slicer3:EM#Old_.282007.29_Tutorial here]</font></big>a |
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| − | The goal of this project is to implement a Slicer3 module for the
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| − | EMSegment brain segmentation algorithm (Pohl et al.). The module
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| − | allows the user to create or edit a collection of parameters and then
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| − | run the algorithm to segment image data. The target audience for this
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| − | module is someone familiar with brain atlases and tissue labels, not a
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| − | computer scientist.
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| − | As of January 1, 2007, the EMSegment module is substantially complete
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| − | and has been checked into the Slicer3 SVN repository. It was
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| − | previewed at the December 2006 NAMIC meeting in Clifton Park and will
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| − | be a demonstration at the NAMIC All-Hands meeting in Salt Lake City on
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| − | Wednesday 10 January 2007. Future work includes adding advanced and
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| − | experimental algorithm parameters, improving visualization of
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| − | parameter settings, and incorporating tissue labels from a controlled
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| − | vocabulary.
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| − | =Contacts=
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| − | *MIT/BWH: Kilian Pohl (pohl@csail.mit.edu)
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| − | *Kitware: Brad Davis (brad.davis@kitware.com)
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| − | =Project Description=
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| − | As stated above, the goal of this project is to provide the
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| − | functionality of the EMSegment algorithm as a Slicer3 module. A
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| − | similar EMSegment module is available in Slicer2.6. The intent of
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| − | this project is to implement a Slicer3 module with similar | |
| − | functionality while also improving the graphical user interface (GUI).
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| − | While the GUI and data structure (MRML) code was completely rewritten
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| − | for the Slicer3 module, the algorithm code was not modified.
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| − | ==High-level Module Description==
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| − | The purpose of the module is to build a template that can be used to | |
| − | segment new image data. The template is composed of atlas data and a
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| − | non-trivial collection of parameters for the EMSegment algorithm. It
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| − | is the user's job to specify the parameters so that the template is
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| − | effective for segmenting a particular target image or image pair
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| − | (e.g., T1 and T2 weighted MR images from a particular scanner).
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| − | Once the parameters are specified, the target images are segmented
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| − | using the EM Segmentation algorithm (Pohl et al.). If the results are
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| − | satisfactory, the template is saved and can be used later to segment
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| − | new images (via the GUI or batch processing). If the results are
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| − | unsatisfactory, the parameters can be modified and the segmentation
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| − | re-run.
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| − | One important aspect of the project is the workflow wizard. This
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| − | wizard simplifies the module by dividing the complicated template
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| − | specification task into a number of smaller, intuitive steps.
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| − | ==Steps in EMSegment Workflow==
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| − | *1/8 Define Parameters Set: Select parameter set or create new parameters
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| − | *2/8 Define Hierarchy: Define a hierarchy of anatomical structures
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| − | *3/8 Assign Atlas: Assign atlases for anatomical structures
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| − | *4/8 Select Target Images: Choose the set of images that will be segmented
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| − | *5/8 Specify Intensity Distributions: Define intensity distribution for each anatomical structure
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| − | *6/8 Edit Node-based Parameters: Specify node-based segmentation parameters
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| − | *7/8 Edit Registration Parameters: Specify atlas-to-target registration parameters
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| − | *8/8 Run Segmentation: Save work and apply EM Algorithm to segment target images
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| − | ==Status==
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| − | A version of the Slicer3 EMSegment module has been completed and
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| − | checked into the Slicer3 SVN repository. Example data have been
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| − | packaged and will soon be available from this wiki page. A tutorial is
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| − | under development and will be presented at the January 2007 NAMIC
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| − | All-Hands Meeting by K. Pohl and B. Davis.
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| − | While there is a completed working version of the module it will
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| − | likely be under development for some time. The primary future
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| − | development efforts will be for (1) bug fixing, (2) adding new
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| − | functionality, (3) modifying the underlying code to make better use of
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| − | the evolving Slicer3 base functionality.
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| − | ===Completed===
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| − | *finalize workflow description (Kilian, Wendy, Brad)
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| − | *define new MRML node structure (Kilian, Brad)
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| − | *implement workflow wizard (Sebastien, Luis)
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| − | *document workflow wizard and write tutorial (Sebastien)
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| − | *implement core MRML classes/attributes (Brad)
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| − | *implement logic class that manages MRML nodes and provides API to GUI (Brad)
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| − | *implement user interface for each wizard step (Yumin, Sebastien)
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| − | *create example data and parameter set (Kilian, Brad)
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| − | *port algorithm code from Slicer2 (Brad)
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| − | ===In Progress===
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| − | *create tutorial (Kilian, Brad)
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| − | ===Future Work===
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| − | *run algorithm in a different thread (with progress bars)
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| − | *incorporate rules for when user may go to next step in workflow
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| − | *add registration to module
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| − | *simplified interface---only load template, load images, start segmentation (like EMAtlasBrainClassifier)
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| − | *add standardized tissue labels; need to elaborate on specification
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| − | *intensity distribution widget
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| − | *incorporate PCA parameters into GUI
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| − | *incorporate Class Interaction Matrix parameters into GUI
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| − | ==Implementation Details==
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| − | The module is implemented as a programmatic Slicer3 module because it
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| − | requires a large degree of interaction with the user, the data stored
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| − | in the MRML tree, and the Slicer3 GUI itself. Because the MRML node
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| − | structure is rather complicated (for example the anatomical tissue
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| − | hierarchy and a large number of interdependent nodes) the Logic class
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| − | is solely responsible for maintaining and accessing these nodes. The
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| − | Logic class provides an API that the GUI code uses to access and
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| − | modify data. The Logic class also wraps the algorithm code itself.
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| − | =EMSegment Tutorial=
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| − | To try out the module with the tutorial data:
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| − | #build the latest version of Slicer3
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| − | #download and untar the data file below (it is approximately 43 megabytes zipped and 329 megabytes unzipped)
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| − | #start Slicer3
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| − | #choose File->Import Scene... and select the file EMSegmentTutorial/Data/EMSegmentTutorialTemplate.mrml from the location where you untared the data
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| − | ##a number of images and MRML nodes will be loaded, this may take some time depending on the speed of you computer and file access
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| − | #in Slicer3 change to the EMSegment module
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| − | #in step 1 of the module make sure that parameter node 100 is selected (that is the one that was loaded in the previous step)
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| − | #use the "Next" and "Back" buttons to navigate through the module, viewing and updating parameters as you go
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| − | ##Note: no parameters need to be modified to run the segmentation using the default tutorial settings
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| − | #on step 8/8, select "Run" and the segmentation will start
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| − | ##the segmentation takes approximately 2.5 minutes on a dual core Pentium with 2 gigabytes of memory
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| − | ##by default the resulting segmentation is saved in the Segmentation_Result image
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| − | [[Media:EMSegmentTutorial_05Jan07.tgz | Tutorial Data 05 Jan 07]]
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