2010 Winter Project Week Spine Segmentation Module in Slicer3
MRI slice and 3D rendering showing spine segmentation results for surgical treatment of disk herniation. (video)
3D Slicer's Spine Segmentation module was presented at the NA-MIC Project Week in Salt Lake City, Jan 4-10, 2010.
- Sylvain Jaume (MIT)
- Martin Loepprich (University of Heidelberg)
- Ron Kikinis, Steve Pieper (BWH)
- Polina Golland (MIT), Ehud Schmidt (BWH)
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.
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.
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.
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 right image shows a disc that protrudes into the vertebral foramen and pinches the nerve bundles as they exit the spine.
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. The image on the right shows the spine overlaid on the MRI image.
This patient-specific illustration can help the surgeon during a minimally invasive intervention on the herniated disc. The image on the right shows an herniated disc that protrudes into the vertebral foramen and reduces the opening for the nerve bundles and the cerebro-spinal fluid (CSF).
The following video shows the segmentation of a herniated disc from MRI using 3D Slicer
- 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