Carve Method - 3d Slicer/Slicer Morph Segmentation Method

0:00 Downloading Files from Morphosource & Initial File Organization/Extraction
4:12 Opening Slicer Morph & Setup
5:28 Segmenting Entire Skeleton/Thresholding
7:50 Segmenting Femur Using Carve Method
8:46 (Skip to this point if you are already familiar with 3d Slicer)
14:55 Cleaning up the Ends of the Bone
24:50 Saving 3d Slicer file as a Scene/Medical Reality Bundle
27:05 Exporting Segments to Meshlab

This video shows a method of segmentation which is less computationally intensive, and produces smoother bones. I found this method to be useful because fill between slices can result in bones which have holes inside, and fill between slices is prone to making regular computers crash. I hope this is helpful :)

STEPS:

1. Threshold Skeleton
2. Create new segment - Select Editable Area inside skeleton and allow overlap
3. Use Circle Brush making sure it is big enough to select the entirety of the bone of interest.
4. Scissors - trace bone of interest (make sure to select “erase outside”)
5. Scissors, “erase inside” to remove areas closer to the bone
6. Use the Erase tool to focus on removing the interactions between adjacent bones. Use a small diameter sphere to paint, and make the diameter around the size of the bone wall.
Use the 3d view to see what you are doing and the 2d view to see if the area is a part of the same bone. Toggle the segment on and off also.
7. Then go back in with the cut tool to remove disconnected or “floating” pieces.
8. Fill in areas which might have been removed using small diameter sphere and 2d paint
(I skipped step 9, because I was happy with the segments, although if you accidentally remove too much these can help to fix the segment)
9. Painting & using Fill between slices can be applied to correct these small errors
Export to meshlab…