|
|
| (66 intermediate revisions by 3 users not shown) |
| Line 1: |
Line 1: |
| − | =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 |
| − | | |
| − | The goal of this project is to implement a Slicer3 module for the
| |
| − | EMSegment brain segmentation algorithm (Pohl et al.). The module
| |
| − | allows the user to create or edit a collection of parameters and then
| |
| − | run the algorithm to segment image data. The target audience for this
| |
| − | module is someone familiar with brain atlases and tissue labels, not a
| |
| − | computer scientist.
| |
| − | | |
| − | As of January 1, 2007, the EMSegment module is substantially complete
| |
| − | and has been checked into the Slicer3 SVN repository. It was
| |
| − | previewed at the December 2006 NAMIC meeting in Clifton Park and will
| |
| − | be a demonstration at the NAMIC All-Hands meeting in Salt Lake City on
| |
| − | Wednesday 10 January 2007. Future work includes adding advanced and
| |
| − | experimental algorithm parameters, improving visualization of
| |
| − | parameter settings, and incorporating tissue labels from a controlled
| |
| − | vocabulary.
| |
| − | | |
| − | =Contacts=
| |
| − | | |
| − | *MIT/BWH: Kilian Pohl (pohl@csail.mit.edu)
| |
| − | *Kitware: Brad Davis (brad.davis@kitware.com)
| |
| − | | |
| − | =Project Description=
| |
| − | | |
| − | As stated above, the goal of this project is to provide the
| |
| − | functionality of the EMSegment algorithm as a Slicer3 module. A
| |
| − | similar EMSegment module is available in Slicer2.6. The intent of
| |
| − | this project is to implement a Slicer3 module with similar | |
| − | functionality while also improving the graphical user interface (GUI).
| |
| − | While the GUI and data structure (MRML) code was completely rewritten
| |
| − | for the Slicer3 module, the algorithm code was not modified.
| |
| − | | |
| − | ==High-level Module Description==
| |
| − | | |
| − | 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
| |
| − | non-trivial collection of parameters for the EMSegment algorithm. It
| |
| − | is the user's job to specify the parameters so that the template is
| |
| − | effective for segmenting a particular target image or image pair
| |
| − | (e.g., T1 and T2 weighted MR images from a particular scanner).
| |
| − | | |
| − | Once the parameters are specified, the target images are segmented
| |
| − | using the EM Segmentation algorithm (Pohl et al.). If the results are
| |
| − | satisfactory, the template is saved and can be used later to segment
| |
| − | new images (via the GUI or batch processing). If the results are
| |
| − | unsatisfactory, the parameters can be modified and the segmentation
| |
| − | re-run.
| |
| − | | |
| − | One important aspect of the project is the workflow wizard. This
| |
| − | wizard simplifies the module by dividing the complicated template
| |
| − | specification task into a number of smaller, intuitive steps.
| |
| − | | |
| − | ==Steps in EMSegment Workflow==
| |
| − | *1/8 Define Parameters Set: Select parameter set or create new parameters
| |
| − | *2/8 Define Hierarchy: Define a hierarchy of anatomical structures
| |
| − | *3/8 Assign Atlas: Assign atlases for anatomical structures
| |
| − | *4/8 Select Target Images: Choose the set of images that will be segmented
| |
| − | *5/8 Specify Intensity Distributions: Define intensity distribution for each anatomical structure
| |
| − | *6/8 Edit Node-based Parameters: Specify node-based segmentation parameters
| |
| − | *7/8 Edit Registration Parameters: Specify atlas-to-target registration parameters
| |
| − | *8/8 Run Segmentation: Save work and apply EM Algorithm to segment target images
| |
| − | | |
| − | ==Status==
| |
| − | | |
| − | A version of the Slicer3 EMSegment module has been completed and
| |
| − | checked into the Slicer3 SVN repository. Example data have been
| |
| − | packaged and will soon be available from this wiki page. A tutorial is
| |
| − | under development and will be presented at the January 2007 NAMIC
| |
| − | All-Hands Meeting by K. Pohl and B. Davis.
| |
| − | | |
| − | While there is a completed working version of the module it will
| |
| − | likely be under development for some time. The primary future
| |
| − | development efforts will be for (1) bug fixing, (2) adding new
| |
| − | functionality, (3) modifying the underlying code to make better use of
| |
| − | the evolving Slicer3 base functionality.
| |
| − | | |
| − | ===Completed===
| |
| − | | |
| − | *finalize workflow description (Kilian, Wendy, Brad)
| |
| − | *define new MRML node structure (Kilian, Brad)
| |
| − | *implement workflow wizard (Sebastien, Luis)
| |
| − | *document workflow wizard and write tutorial (Sebastien)
| |
| − | *implement core MRML classes/attributes (Brad)
| |
| − | *implement logic class that manages MRML nodes and provides API to GUI (Brad)
| |
| − | *implement user interface for each wizard step (Yumin, Sebastien)
| |
| − | *create example data and parameter set (Kilian, Brad)
| |
| − | *port algorithm code from Slicer2 (Brad)
| |
| − | | |
| − | ===In Progress===
| |
| − | *create tutorial (Kilian, Brad)
| |
| − | | |
| − | ===Future Work===
| |
| − | *run algorithm in a different thread (with progress bars)
| |
| − | *incorporate rules for when user may go to next step in workflow
| |
| − | *add registration to module
| |
| − | *simplified interface---only load template, load images, start segmentation (like EMAtlasBrainClassifier)
| |
| − | *add standardized tissue labels; need to elaborate on specification
| |
| − | *intensity distribution widget
| |
| − | *incorporate PCA parameters into GUI
| |
| − | *incorporate Class Interaction Matrix parameters into GUI
| |
| − | | |
| − | ==Implementation Details==
| |
| − | | |
| − | The module is implemented as a programmatic Slicer3 module because it
| |
| − | requires a large degree of interaction with the user, the data stored
| |
| − | in the MRML tree, and the Slicer3 GUI itself. Because the MRML node
| |
| − | structure is rather complicated (for example the anatomical tissue
| |
| − | hierarchy and a large number of interdependent nodes) the Logic class
| |
| − | is solely responsible for maintaining and accessing these nodes. The
| |
| − | Logic class provides an API that the GUI code uses to access and
| |
| − | modify data. The Logic class also wraps the algorithm code itself.
| |
| − | | |
| − | =EMSegment Tutorial=
| |
| − | | |
| − | To try out the module with the tutorial data:
| |
| − | #build the latest version of Slicer3
| |
| − | #download and untar the data file below (it is approximately 43 megabytes zipped and 329 megabytes unzipped)
| |
| − | #start Slicer3
| |
| − | #choose File->Import Scene... and select the file EMSegmentTutorial/Data/EMSegmentTutorialTemplate.mrml from the location where you untared the data
| |
| − | ##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
| |
| − | #in Slicer3 change to the EMSegment module
| |
| − | #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)
| |
| − | #use the "Next" and "Back" buttons to navigate through the module, viewing and updating parameters as you go
| |
| − | ##Note: no parameters need to be modified to run the segmentation using the default tutorial settings
| |
| − | #on step 8/8, select "Run" and the segmentation will start
| |
| − | ##the segmentation takes approximately 2.5 minutes on a dual core Intel processor with 2 gigabytes of memory
| |
| − | ##by default the resulting segmentation is saved in the Segmentation_Result image
| |
| − | | |
| − | [[Media:EMSegmentTutorial_05Jan07.tgz | Tutorial Data 05 Jan 07]]
| |
