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Gallery of New Features

Module Name

EM Segment BatchMake

EM Segment BatchMake module GUI

General Information

Module Type & Category

Type: CLI

Category: Batch Processing

Authors, Collaborators & Contact

  • Authors: Stephen Aylward, Julien Finet
  • Contact: stephen.aylward at

Module Description

This module is the BatchMake version of EM Segment Simple, a simplified "one-click" GUI interface for the EMSegment Command-line Executable. The interface is simple because the number of required command-line parameters is minimized, and it is flexible because any EM algorithm parameter can be modified, within the MRML scene, via the EMSegment GUI interface. The batch processing feature allows the user to run the EMSegment module on multiple patients. By defining a patient root directory and a mask to iterate through the patients, EMSegment simple will be run for each images found in the matched images.


MRML Scene = the mrml file name that contains all the parameters previously defined with EMSegment Template Builder module
Data directory = where the patients images are ( T1, T2 images ) Directory mask = to be a valid input, the patients directories located in "Data directory" must match the mask Target 1 mask = T1 image mask that must be matched inside the patients directories Target 2 mask = T2 image mask that must be matched inside the patients directories Output directory = where the results are saved

Examples, Use Cases & Tutorials

For the following file tree:

  • Images
    • EMSegmentParameters.mrml
    • Atlas
      • ...
    • Patient1
      • Patient1.txt
      • Patient1-T1.mha
      • Patient1-T2.mha
    • Patient2
      • Patient2.txt
      • Patient2-T1.mha
      • Patient2-T2.mha
    • Patient3
      • Patient3.txt
      • Patient3-T1.mha
      • Patient3-T2.mha
  • Results

Parameters are:
MRMLScene: "Images/EMSegmentParameters.mrml"
Data Directory: "Images"
Directory Mask: Patient*
Target 1 Mask: *T1.mha
Target 2 Mask: *T2.mha
Output directory: "Results"

Quick Tour of Features and Use

To run the module on a condor grid, open the BatchMake parameter group and choose "condor" as running mode. Make sure your data are accessible by all the condor machines.



EMSegment Simple module

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: EMSegmentBatchMakeModule.cxx

XML Description: EMSegmentBatchMakeModule.xml


More Information


This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from National Centers for Biomedical Computing.