Difference between revisions of "2011-Challenge:Segment-a-spine"

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=The Challenge=
 
=The Challenge=
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*Provide a tool in 3D Slicer which will segment  
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*Provide a tool in 3D Slicer which will segment vertebrae. It is expected that each vertebra is individually and fully labelled.
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**vertebrae. It is expected that each vertebra is individually labelled and
 
 
*the algorithm can be developed using the data below
 
*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 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 can be semi-automated. It is acceptable to ask the user to point to one or more vertebrae or other structures.  
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*The algorithm must comply with [http://www.slicer.org/slicerWiki/index.php/Documentation-Rons-Rules-For-Tools "Rons Rules For Tools"].
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*The algorithm must comply with [https://www.slicer.org/wiki/Documentation-Rons-Rules-For-Tools "Rons Rules For Tools"].
  
 
=Deliverables=
 
=Deliverables=
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*Deliver your solution to Ron by May 31 2011
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*Deliver your solution to Ron (contact by email) by May 31 2011
−
*The best solution will be awarded with one price of USD 500
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**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":
 
*Definition of "best":
 +
**Compliant with Rons Rules for Tools. Slicer license strongly preferred.
 
**Outer boundaries of the vertebral body correspond to the visible boundaries
 
**Outer boundaries of the vertebral body correspond to the visible boundaries
 
**Clean separation from adjacent vertebrae, ribs (if present) and intervertebral disks
 
**Clean separation from adjacent vertebrae, ribs (if present) and intervertebral disks
−
**Full segmentation of the transverse, spinous, and other processes
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**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.
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** During the test phase thoracic or lumbar vertebrae will be used. The cervical vertebrae will not be used.
  
 
=Sample data set=
 
=Sample data set=
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*[[Media:CT crop.zip|See 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.
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*[[Media:CT crop.zip|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 [[RSNA2010.PlanningLog#Demos_for_the_Slicer_booth|this table]] is the original location.
 
**The bottom case in [[RSNA2010.PlanningLog#Demos_for_the_Slicer_booth|this table]] is the original location.
 
*[[media:2009-03-03-722LungCT-4.nrrd|Lung CT data set]]: This is a data set from a different subject.
 
*[[media:2009-03-03-722LungCT-4.nrrd|Lung CT data set]]: This is a data set from a different subject.
 
*[[media:COPDCases.zip|Lung CT data sets (3 cases) with COPD]]: These are three subjects with different degree of COPD.
 
*[[media:COPDCases.zip|Lung CT data sets (3 cases) with COPD]]: These are three subjects with different degree of COPD.
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 +
 +
  
 
[[image:2010AbdominalAtlasBones.png|right|350px|Individual vertebrae have been manually segmented in the abdominal atlas]]
 
[[image:2010AbdominalAtlasBones.png|right|350px|Individual vertebrae have been manually segmented in the abdominal atlas]]
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*http://en.wikipedia.org/wiki/Lumbar_vertebrae
 
*http://en.wikipedia.org/wiki/Lumbar_vertebrae
 
*http://en.wikipedia.org/wiki/Sacrum
 
*http://en.wikipedia.org/wiki/Sacrum
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[[image:RadnosticsSpineSegmentationSample.jpg|right|300px|Radnostics Spine Segmentation]]
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=Winning Project=
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The winning project of the 2011 segment-a-spine-challenge is
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[http://wiki.na-mic.org/Wiki/index.php/2011_Summer_Project_Week_Spine_Segmentation_And_Osteoporosis_Screening_CT Radnostics Spine Segmentation And Osteoporosis Screening in CT] by
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*[http://radnostics.com/default.aspx Radnostics]: [mailto:Anthony.Blumfield@Radnostics.com Anthony Blumfield]
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*[http://www.einstein.yu.edu/home/default.asp Albert Einstein College of Medicine]: [http://www.einstein.yu.edu/home/faculty/profile.asp?id=10350 Einat Blumfield, MD]

Latest revision as of 17:34, 10 July 2017

Home < 2011-Challenge:Segment-a-spine
Back to 2010 AHM agenda
Volume rendering of the spine in the challenge data set

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



Individual vertebrae have been manually segmented in the abdominal atlas

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:



Radnostics Spine Segmentation


Winning Project

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

Radnostics Spine Segmentation And Osteoporosis Screening in CT by

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