2011-Challenge:Segment-a-spine

Back to 2010 AHM agenda

Introduction

• This is the first in a series of challenges which aim at improving our set of robust interactive segmentation tools.

The Challenge

• Provide a tool in 3D Slicer which will segment vertebrae. It is expected that each vertebra is individually and fully labelled.
• the algorithm can be developed using the data below
• the algorithm will be tested using a different ct data set of comparable quality.
• The algorithm can be semi-automated. It is acceptable to ask the user to point to one or more vertebrae or other structures.
• The algorithm must comply with "Rons Rules For Tools".

Deliverables

• Deliver your solution to Ron (contact by email) by May 31 2011
  • Plug-in for Slicer using the Slicer license
  • Directions on how to use

• The best solution will be awarded a prize of USD 500.-
• Definition of "best":
  • Compliant with Rons Rules for Tools. Slicer license strongly preferred.
  • Outer boundaries of the vertebral body correspond to the visible boundaries
  • Clean separation from adjacent vertebrae, ribs (if present) and intervertebral disks
  • Full segmentation of the transverse, spinous, and other processes.
  • 2-3 vertebrae will be segmented by Ron on his laptop using your tool on Rons CT data sets. The data sets will be of a quality comparable to the test data sets.
  • During the test phase thoracic or lumbar vertebrae will be used. The cervical vertebrae will not be used.

Sample data set

• See example of a volume of interest which is cropped from the full data set. For reference, L1 has been labeled. Use File/Load scene to load the volume into Slicer. The size of the download is 70MB and contains the original data set as well.
  • The bottom case in this table is the original location.
• Lung CT data set: This is a data set from a different subject.
• Lung CT data sets (3 cases) with COPD: These are three subjects with different degree of COPD.

Atlas reference

If you need anatomical knowledge, please download [1] which contains some individually labeled vertebrae.

To learn about regional differences among healthy vertebrae see the following wikipedia entries:

• http://en.wikipedia.org/wiki/Vertebrae
• http://en.wikipedia.org/wiki/Cervical_vertebrae
• http://en.wikipedia.org/wiki/Thoracic_vertebrae
• http://en.wikipedia.org/wiki/Lumbar_vertebrae
• http://en.wikipedia.org/wiki/Sacrum

Winning Project

The winning project of the 2011 segment-a-spine-challenge is

Radnostics Spine Segmentation And Osteoporosis Screening in CT by

• Radnostics: Anthony Blumfield

• Albert Einstein College of Medicine: Einat Blumfield, MD