Vertebrae and Vmtk centerlines

[Manoj Shankar]

Hi All,

I'm trying to compute center lines for the Vertebrae , i did follow the instructions in documentation and tutorials but i was unable to get the answer,In theory computing centerlines for vascular segment is same as computing for bones ,if not can you please suggest a solution to compute centerlines for a bone.I'm importing the surface of bone using .stl file. guys help me out im totally new to vmtk 

Thanks in Advance :)

[andra...@gmail.com]

To get spinal curve, the most common approach is to drop points at the tip of the spinous process of each vertebra (in CT) or along the spinal canal (in CT or MRI) and connect them with a spline.

 

You only need centerline extraction if you segment something. VMTK is quite robust, so it can extract centerline of anything that vaguely resembles a tube shape. In the spine, the spinal canal is a good choice. You could segment the vertebral bodies, too but then you would probably want to solidify (if you want to extract a single curve and not a network).

 

All these are already implemented in 3D Slicer:

 

Without segmentation:

• Curve based on spinous process tips on CT: Use volume rendering to see the spinal column, create a markups curve, and click on tips of the spinous process.
• Curve based on spinal canal: Create a markups curve and click in the middle of the spinal canal, approximately on in each vertebra.

 

With segmentation:

• Based on spinal canal: You can segment the spinal column on CT almost fully automatically – see here: https://discourse.slicer.org/t/drawing-line-through-spinal-canal-using-ct/12384/4. On MRI, it may be a bit harder, but probably “Grow from seeds” effect in Segment Editor module can work well enough.
• Based on bones: You can very easily segment the vertebra on CT (Threshold effect), cut off the ribs (Scissors effect), and then fill internal holes (using WrapSolidify effect, provided by SurfaceWrapSolidify extension)
• After segmentation is complete, you can use “Extract centerline” module (provided by SlicerVMTK extension) to extract centerline curve

 

Once you have centerline curve, you can use Curved Planar Reformat module (provided by Sandbox extension) to straighten the curve and/or compute mapping between the spine curve and a straight line.

 

This allows you to make measurements, as shown here:

 

https://discourse.slicer.org/t/how-to-make-fiducial-points-placed-in-curved-planar-reformatted-image-appear-in-the-original-image/12189/4?u=lassoan

 

Or you can straighten the entire skeleton as shown here:

 

https://discourse.slicer.org/t/how-to-implement-cpr-curved-plannar-reconstruction-from-centerline/9456/7

 

Andras

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