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Target Outcome

Volumetric reconstruction of a tissue of interest:

• as an image volume, and
• as a surface representation

Prerequisites

Include(Infrastructure/AuxiliarySoftware, "Infrastructure", 2, from="= Image Analysis & Segmentation =", to="= Geometry & Mesh Generation & Manipulation =")

Previous Protocols

For more details, see ["Specifications/ExperimentationAnatomicalImaging"].

Protocols

Input

Set(s) of MRI in NIFTI format

Procedures

-- ["aerdemir"] DateTime(2013-12-17T13:25:32Z) This section may list general purpose procedures and alternatives to utilize the same input to reach the same output. Procedures optimized for specific tissues should also be provided in here.

Overall Process

• Download desired image volume for the desired specimen; the data should be in NIFTI format.

• Load the desired image volume to a preferred image segmentation & analysis software faithful to data coordinate system.

• Tissue of interest can be segmented by manually painting over its boundaries or using automated or semi-automated algorithms available in the image segmentation & analysis software.

  • Segmentation in process should be saved in the relevant repository area specific to the specimen and segmentation results. The file format should be NIFTI and file naming convention should rely on tissue labeling described in ["Specifications/DataManagement"], e.g., oks001-fmb-01.nii, indicating the segmentation for femur bone of the Open Knee(s) - Specimen 1, the appended number indicates the segmentation label (to accommodate multiple segmentations of the same volume by others).
  • The boundaries of the tissue volume obtained from segmentation should not be smoothed.
  • Segmented volume can be loaded to other image sets to evaluate and correct for boundaries.
• After completion of the segmentation, the volume should be exported as a triangulated surface (without smoothing) in STL format, e.g. oks001-fmb-01.stl

Tissue Specific Considerations

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.

Bones

Tissue labels include FMB (femur), TBB (tibia), FBB (fibula), PTB (patella).

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).

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).

Ligaments & Tendons

Ligament segmentation should be informed by bone segmentation, i.e. subtraction of bone volume to trim insertion areas.

Tissue labels include ACL, PCL, LCL, PTL, QAT, etc.

Output

• Volume of tissue of interest as a binary image aligned with original MRI coordinate system (raw, without filtering and smoothing)
• Surface representation of tissue of interest in STL format in MRI coordinate system (raw, without filtering and smoothing)