Slicer3:EM

Project Summary

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.

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.

Contacts

• MIT/BWH: Kilian Pohl (pohl@csail.mit.edu)
• Kitware: Brad Davis (brad.davis@kitware.com)

EMSegment Workflow Module

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.

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

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

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

Steps in EMSegment Workflow

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

Status

A version of the Slicer3 EMSegment workflow module has been completed and checked into the Slicer3 SVN repository. Example data have been packaged with a tutorial and are available from this wiki page. Tutorial sessions were presented at the January 2007 and 2008 NAMIC All-Hand's meetings 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)
• create tutorial (Kilian, Brad)
• intensity normalization (Kilian, Brad)
• atlas-to-target registration (Brad)
• target-to-target registration (Brad)
• command-line interface (Brad)
• regression testing (Brad)
• create new 2008 tutorial(Brad, Kilian)

In Progress

• bug fixes
• intensity distribution widget
• incorporate feedback from NAMIC community into priorities for future work
• segmentation results validation (Sylvain, Brad)
• help text (Kilian, Brad)

Future Work

Major categories:

• Bug fixing
• Ease of use
  • User support
  • Tutorials/Help/Documentation
  • Template Library
• Improved functionality
  • GUI changes
  • Algorithmic & preprocessing improvements

Brad

• Major bug fixes (Brad)
• User support bug fixes & clarifications (Brad)
• Choose to do or redo or not do preprocessing
• Move EMSegment under segmentation
• Make Kilian happy with registration
  • affine atlas registration (most important)
  • maxwell demons registration (symmetric)
  • improved memory and speed for bsplines
• Name associated with input channel
  • make gui/logic changes
• Name associated with structures
  • gui / logic changes
• Input channel smoothing filter
• Propogate parameters inherit from siblings or parent
• Class overview with tree (Brad ask Sebastien)
• Generate surface models (auto generate after run, Brad)
• Wizard buttons not scrolled out of view: maybe move to top (Brad)

Kilian & Others

• Core functionality and algorithm fixes (Kilian)]
• Template library (Katarina, Sonja)
  • current WM/GM/CSF
  • Kilian's TMI atlas paper~12: ask Ron (Martha's data)
  • Hand
  • Cells
  • skull stripping (Katarina)
  • link to list on wiki page
• Step-by-step tutorial (Sonja)
• Name associated with structures
  • establish naming and colormap conventions
• Change log-normal to normal
• Automatic sampling for intensity distros
  • load in sample map
• Intensity distribution widget
• Volume computation
• Help text (Sonja, Kilian)
  • Registration parameters, etc
  • assign target image (order of images is important)
  • papers to read

Other/All

• Merge EMSegment w/ UNC pipeline
• User support (first line of defense, Brad, Kilian)
• Immediate visual feedback (postdoc from Isreal)
  • when adjusting intensity distrubtions
  • when change weights---impact on segmentation
• Rules for wizard transitions---for user support, etc.

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 Command-line Executable

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.

The executable is included in the Slicer3 distribution.

Status

A first version of the EMSegmentCommandLine program is complete. We are currently testing the program with users and may modify the interface.

Interface

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.

The interface is under construction and subject to change; here is the current version.

Example

The EMSegment tutorial data set demonstrates the use of the use of the command line interface. You can download it below. Here are some basic examples:

• Run the executable to see the documentation

$Slicer3-Build/bin/EMSegmentCommandLine --help

• Run the segmentation algorithm on your data

$Slicer3-Build/bin/EMSegmentCommandLine --mrmlSceneFileName $EMSegmentTutorial/Data/EMSegmentTutorialTemplate.mrml --resultVolumeFileName /tmp/segmentation.mhd --targetVolumeFileNames /MyImageDirectory/MyImageT1.mhd,/MyImageDirectory/MyImageT2.mhd --verbose

• Run the segmentation algorithm using an atlas that is aligned to your image data

$Slicer3-Build/bin/EMSegmentCommandLine --mrmlSceneFileName $EMSegmentTutorial/Data/EMSegmentTutorialTemplate.mrml --resultVolumeFileName /tmp/segmentation.mhd --targetVolumeFileNames /MyImageDirectory/MyImageT1.mhd,/MyImageDirectory/MyImageT2.mhd --verbose --atlasVolumeFileNames atlasBackgroundReg_small.mhd,atlasBackgroundReg_small.mhd,atlasCSFReg_small.mhd,atlasGreymatterReg_small.mhd,atlasWhitematterReg_small.mhd

Note that the order of the target and atlas volumes is important---use the order above for the tutorial dataset. Use an order that matches the mrml parameters file if you design a different parameter set.

What Can Go Wrong?

• Shared libraries were not found
  • If your run the executable and shared libraries are not found, then you need to add VTK, ITK, KWWidgets, and Slicer3 build library directories to your path. You can also run the executable using Slicer3 as a wrapper. This method will set up the paths correctly; run it like this:

  $Slicer3-Build/bin/Slicer3 --launch $Slicer3-Build/bin/EMSegmentCommandLine --help

EMSegment Tutorials

2008 Tutorial

These slides and data describe the Slicer3 implementation of the EMSegmenter and demonstrate its use. A recent (7Jan08) version of Slicer3 is required to run the test data.

Slides - Data

Old (2007) Tutorial

NOTE: This version of the tutorial is not compatible with the latest Slicer SVN version. It is compatible with Slicer versions that were released around the Summer Project week 2007. An updated tutorial will be released soon (around the time of the January 2008 All-Hands meeting).

To try out the module with the tutorial data:

1. build the latest version of Slicer3
2. download and untar (or unzip) the data file below (it is approximately 43 megabytes zipped and 329 megabytes unzipped)
3. start Slicer3
4. choose File->Import Scene... and select the file EMSegmentTutorial/Data/EMSegmentTutorialTemplate.mrml from the location where you untared the data
   1. 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
5. in Slicer3 change to the EMSegment module
6. in step 1 of the module make sure that the parameter node "TutorialTemplate" is selected (that is the one that was loaded in the previous step)
7. use the "Next" and "Back" buttons to navigate through the module, viewing and updating parameters as you go
   1. Note: no parameters need to be modified to run the segmentation using the default tutorial settings
8. on step 8/8, select "Run" and the segmentation will start
   1. the segmentation takes approximately 2.5 minutes on a dual core Intel processor with 2 gigabytes of memory
   2. by default the resulting segmentation is saved in the segmentation_result.mhd image

Tutorial: Slides - Data (tgz) - Data (zip)

Screen Shot

EMSegmenter Mini-Tutorials

EMSegmenter Frequently Asked Questions