Connor Lough
loughc@ccf.org

This folder contains a complete segmentation of oks001 as well as segmentation of the registration markers for all the knees. The oks001 segmentation contains the bones (Tibia, Femur, Fibula, Patella), meniscus, and cartilage. The registration markers can be found both in this folder, but also in each individual oks00# folder.

For more information, visit: http://wiki.simtk.org/openknee/Specifications/ImageSegmentation

Labeling:

REG - Registration Markers
TBB - Tibia
FMB - Femur
FBB - Fibula
PTB - Patella

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Further information on Registration Markers:

Volume labels include bone type and marker location, e.g. REG-FM, where REG stands for registration, F for femur, M for medial. In result, potential labels are REG-FM, REG-FL, REG-FA, REG-FP, REG-TM, REG-TL, REG-TA, REG-TP, REG-PS, REG-PL, REG-PM.


For more on placement of markers, visit: http://wiki.simtk.org/openknee/Specifications/SpecimenPreperation

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Further information on Cartilage:

Cartilage segmentation should be informed by bone segmentation, i.e. subtraction of bone volume to trim back surface of cartilage. Tissue labels include FMC (femoral), TBC-M (medial tibial), TBC-L (lateral tibial), PTC (patellar).

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Further information on Menisci:

Menisci segmentation should be informed by cartilage segmentation, i.e. subtraction of menisci volume to match cartilage boundaries. Tissue labels include MNS-M (medial), MNS-L (lateral).

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Methods:

Bones - Used Level Tracing Effect and Paintbrush, then Grow Cut Effect
Cartilage - 
Meniscus -
Registration Markers - Level Tracing Effect, Cleaned up with paint brush, then Grow Cut Effect

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Grow Cut Notes:

Highlight in each view
Highlight beginning, middle, and end. Plus, where you can no longer see structure.
Highlight area surrounding structure with seperate color and then use label change effect to change to background at the end.

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File Types:

.nii - 
.mrml - 
.nrrd - 
.png -