From Slicer Wiki
Jump to: navigation, search
Home < Modules:EMDTIClustering-Documentation-3.6

Return to Slicer 3.6 Documentation

Gallery of New Features

Module Name

EM Fiber Clustering Module

Module interface
Trajectories colored by their cluster ID

For version 3.6.2 and beyond, please refer to DTI Fiber Clustering Module-Documentation-3.6.2. The new version has two new capabilities: Atlas-based seeding and multi-subject tract-based quantitative analysis.

General Information

Module Type & Category

Type: CLI

Category: Clustering

Authors, Collaborators & Contact

  • Mahnaz Maddah
  • James Miller
  • Contact: Mahnaz Maddah, mmaddah [at]

Module Description

This module clusters a set of input trajectories into a number of bundles, generates arc length parameterization by establishing the point correspondences and reports diffusion parameters along the bundles as well as the membership probability of each trajectory in each cluster. The module requires specification of seed trajectories (or initial centerlines) as representatives of the desired bundles.


Examples, Use Cases & Tutorials

Tutorial and test data can be downloaded from here:

Quick Tour of Features and Use

Here is a list of the panels in the module:

  • IO panel:
 Trajectories                        Input trajectories to be clustered.
 Output Clusters                     Clustered trajecories labeled by their cluster ID.
 Initial Centers                     [optional] Initial center(s). Note that intial centers need 
                                         to be provided by passing either a set of trajectories here or a fiducial list. 
 Fiducials to Pick Initial Centers   [optional] A fiducial list to generate initial center(s). For each fiducial 
                                         in the list the closest trajectory in the input is selected as the initial center. 
 Output Initial Centers              [Optional] Selected initial cluster centers.
 Output Final Centers                [Optional] Final cluster centers, colored by the mean FA value along the bundle 
                                         if "Perform Quantitative Analysis" is flaged .
 Perform Quantitative Analysis       Flag that needs to be marked if quantitative analysis is desired to be done.
 Output Directory                    A directory needs to be specified if performing quantitative analysis.       
 File Prefix Name                    Prefix of the output files generated through tract-oriented analysis. 
 Description of generated CSV files by EM Clustering Module

  • Clustering Parameters:
 Compactness of Fiber Bundles        Parameter between 1 and 5 that specifies the extent of similarity between the 
                                         trajectories of each cluster. Increase the value for more compact bundles.  
  • Advanced Parameters:
 Space Resolution                    Space resolution for distance map calculation.
 Iterations                          Maximum number of EM iterations.
 Maximum Distance                    Maximum distance in mm specifies an upper threshold on the distance of points that 
                                         can contribute to new center formation.


Notes from the Developer(s)

This module is based on the algorithms developped for quantitative analysis of white matter fiber tracts as a part of the author's PhD work: Mahnaz Maddah, Quantitative Analysis of Cerebral White Matter Anatomy from Diffusion MRI, Ph.D. Thesis CSAIL, MIT, September 2008.




On the Dashboard, these tests verify that the module is working on various platforms:

Known bugs

Follow this link to the Slicer3 bug tracker.

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

Source code link

More Information


This work has been supported by NAC.