Difference between revisions of "2010 Winter Project Week Spine Segmentation Module in Slicer3"
Sylvainjaume (talk | contribs) (add .gif extension to filename) |
Sylvainjaume (talk | contribs) (shorten text. remove mention to CSF (b/c not visible in picture)) |
||
Line 2: | Line 2: | ||
<gallery> | <gallery> | ||
Image:Loepprich_Jaume_vertebra_Slicer_Jan2010.png|Our 3DSlicer module provides an automated segmentation of the spine in view of the treatment of disc herniation. [http://www.youtube.com/watch?v=kkAuP80kE8E (video)] | Image:Loepprich_Jaume_vertebra_Slicer_Jan2010.png|Our 3DSlicer module provides an automated segmentation of the spine in view of the treatment of disc herniation. [http://www.youtube.com/watch?v=kkAuP80kE8E (video)] | ||
− | Image:Martin_Loepprich_vertebrae_animation_Jan2010.gif|This 3D rendering shows the L3, L4 and L5 vertebrae | + | Image:Martin_Loepprich_vertebrae_animation_Jan2010.gif|This 3D rendering shows the L3, L4 and L5 vertebrae (pink - top to bottom), the inter-vertebral discs (blue) and the spinal cord (red). |
Image:Sylvain_Jaume_vertebrae_and_discs_Jan2010.png|This 3D rendering shows the nerve bundles surrounded by the cerebro-spinal fluid as they traverse the vertebrae. | Image:Sylvain_Jaume_vertebrae_and_discs_Jan2010.png|This 3D rendering shows the nerve bundles surrounded by the cerebro-spinal fluid as they traverse the vertebrae. | ||
Line 46: | Line 46: | ||
{| | {| | ||
− | + | |[[Image:Sylvain_Jaume_disc_herniation_Jan2010.png|thumb|280px|Back pain is caused by a disc that protrudes into the vertebral foramen and pinches the nerve bundles as they exit the spine.]] | |
− | |[[Image:Sylvain_Jaume_disc_herniation_Jan2010.png|thumb| | ||
|} | |} | ||
Line 60: | Line 59: | ||
{| | {| | ||
− | |[[Image:spine_segmentation_in_slicer_004.png|thumb| | + | |[[Image:spine_segmentation_in_slicer_004.png|thumb|340px|Surface meshes and volumetric meshes of our automatically created model of the CSF. The paths where the nerves exit the spine appear as two roots descending on each side of the spinal column.]] |
− | |[[Image:Sylvain_Jaume_nerve_segmentation_rendering_2009.png|thumb| | + | |[[Image:Sylvain_Jaume_nerve_segmentation_rendering_2009.png|thumb|260px|Results of our automated nerve segmentation algorithm. The 3D rendering shows the nerves exiting the spinal cord and the ganglia.]] |
|} | |} | ||
Revision as of 23:16, 1 February 2010
Home < 2010 Winter Project Week Spine Segmentation Module in Slicer3Our 3DSlicer module provides an automated segmentation of the spine in view of the treatment of disc herniation. (video)
Our 3DSlicer module for automated segmentation was presented at the NA-MIC Project Week in Salt Lake City, Jan 2010.
Key Investigators
- Sylvain Jaume (MIT)
- Martin Löpprich (University of Heidelberg)
- Ron Kikinis, Steve Pieper (BWH)
- Polina Golland (MIT), Ehud Schmidt (BWH)
Objective
We are developing a Slicer module to segment the region within the thecal sac in MRI images of the spine. Our objective is to provide a segmentation and visualization tool to improve the treatment of disc herniation. The structures of interests are the cerebro-spinal fluid (CSF), the discs, the vertebrae and the spinal nerves.
Approach, Plan
Our plan for the project week is to integrate our code into Slicer 3.5. Our code analyzes the intensity profile of different regions in the MRI and automatically defines the optimum region for the CSF.
Progress
The algorithm has been implemented in Slicer 3.5 as an extension module. This volumetric pattern recognition algorithm is fully implemented as a Slicer module using ITK and VTK. The module has been tested on data sets acquired at Brigham and Women's Hospital.
Illustrations
The cause of back pain is the pressure of the herniated disc onto the spinal nerves. The herniated disc pushes the canal for the cerebro-spinal fluid (CSF). The resulting pressure on the nerve bundles can cause severe discomfort and even permanent disability if not treated.
The CSF has a double role: it acts as a lubricant between the vertebrae and as a mechanical insulation to protect the nerves from outside shocks. The main challenge is to perform the segmentation in a fully automated way.
Video
The following video shows the segmentation of a herniated disc from MRI using 3D Slicer
Media:Herniated_disc_segmentation_using_3DSlicer.ogg
References
- Expectation-Maximization segmentation: EMSegment module in Slicer
- Creation of a statistical atlas: AtlasCreator module in Slicer
- MRI bias field correction: MRIBiasFieldCorrection module in Slicer
- More references: Sylvain Jaume at MIT CSAIL