2014 Project Week:Slicer Based Surface Template Estimation

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Key Investigators

  • JHU: Saurabh Jain
  • Isomics: Steve Pieper
  • Iowa: Hans Johnson
  • Utah: Josh Cates

Project Description


Develop a Slicer interface to the remote processing service for template estimation of sub cortical structures offered by Center for Imaging Science (CIS) through our ftp site.

Approach, Plan

  • The template estimation is performed using a variant of the approach described in:
J. Ma, M. I. Miller, and L. Younes, 
“A Bayesian Generative Model for Surface 
Template Estimation,” Intl. J. Bio. Img., 
vol. 2010, Article ID 974957. 
  • The pipeline accepts surfaces stored in the BYU format, or binary masks stored in the ANALYZE format. The processing is done on one of the clusters available to CIS, and upon completion the user receives an e-mail with a link to the results stored on the ftp site.
  • We plan to provide an interface to browse the surfaces in Slicer, and an interface to send jobs to and receive results from the remote processing server.


  • Created a simple interface, which accepts the directory location, and e-mail address (which must be registered with http://www.MRIStudio.org), and sends the remote processing job if the directory contains .byu files.
  • To receive the results copy the md5 checksum from the e-mail, which reports the job completion, to the md5 box in slicer and hit receive.
  • In the near future, make it more user friendly, and put it up on the extension manager.
  • Hans shared datasets for testing: