2011 Summer Project Week Plastimatch for EMSegmenter

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Home < 2011 Summer Project Week Plastimatch for EMSegmenter

Integrating Plastimatch into the EMSegmenter

Key Investigators

  • University of Pennsylvania: Dominique Belhachemi
  • University of Pennsylvania: Kilian Pohl
  • University of Pennsylvania: Daniel Haehn
  • MGH: Greg Sharp


Objective

During the EMSegmenter's pre-processing we have to register our internal atlas to the subject scan. Currently we support two registration tools:
1. BRAINSFit
2. CMTK

We would like to add "plastimatch" to this list.


Approach, Plan

Investigating the commandline interface of plastimatch.
Find the right parameter for our use cases.


Progress

We added plastimatch to the EMSegmenter GUI and integrated some base code to call plastimatch.
Fixed compiler issue on i386 for stand-alone plastimatch and Slicer's plastimatch extension.
Now we have a nighly plastimatch-slicer extension for Linux 32 bit.
We had to add an option to plastimatch's reformat command to specify the target grid.

Open: Find the right parameter for our CT use cases.

References

http://plastimatch.org/
https://www.slicer.org/wiki/EMSegmenter-Tasks

Delivery Mechanism

This work will be delivered to the NAMIC Kit as part of the EMSegmenter module.