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

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

Segmentation Specific Procedures

-- ["ogad"] DateTime(2015-07-16T18:36:39Z)

* Using 3DSlicer for segmentation:

Opening data
- File => Add Data => [Select MRI file in NIFTI format]
- Open drop-down menu from toolbar for list of modules.
- Select Editor to edit the labelmap (a volume representation of highlighted regions).
- One can manually segment bones for every slice, or use Growth Cut Effect and Threshold Effect.
Editor Module
- Applying Growth Cut Effect:
  - Use Draw Effect or Paint Effect to highlight anatomy of interest (foreground) using specific label (label1).
  - Use Draw Effect or Paint Effect to highlight area around anatomy of interest (background) with different label (label2).
    - See figure below for example of segmented slice with the label1 represented as yellow and label2 represented as blue. attachment:tibia.png
  - Repeat for five slices at varying depths for each view (coronal, sagittal, axial).
  - Use Growth Cut Effect to complete segmentation of bone. (Apply)
  - Remove background by using Change Label Effect; select label2 as input and background [0] as output. (Apply)
  - Manually segmentation to clean up results of Growth Cut Effect.
  - ** For more information on Growth Cut Effect refer to the 3DSlicerWiki [http://www.slicer.org/slicerWiki/index.php/Modules:GrowCutSegmentation-Documentation-3.6].
- Applying Threshold Effect for bones:
  - Label1:
    - Threshold Effect: Threshold Range - mid 130 to mid 180 (Apply)
    - Remove Islands Effect: Morphology Method
    - Save Islands Effect: Select bone of interest
    - Erode and Save Islands Effect: Repeated consecutively until areas of disinterest removed
  - Label2:
    - Threshold Effect: Threshold Range - lower 40 to mid 110 (Apply)
    - Remove Islands Effect: Morphology Method
    - Save Islands Effect: Select bone of interest
    - Erode and Save Islands Effect: Repeated consecutively until areas of disinterest removed
    - Paint Effect: Manual segmentation to add/remove from label
  - Combine Label1 and Label2:
    - Paint Effect: Manual segmentation to add/remove from label
- Generating raw volume from label for anatomy of interest.
  - In Make Model Effect, choose model name, deselect smooth model and select apply.
  - Creates vtk file.
  - To save as surface representation, save vtk file as STL file.
Tips and Shortcuts using 3DSlicer:
- In Editor Mode:
  - 'c' to open list of labels, type # of label id and enter to switch labels quickly
  - 'z' to undo
  - 'y' to redo
  - 'd' for Draw Effect
  - 'p' for Paint Effect
  - 'e' to erase from label
  - arrow keys to move forward/background a slice
  - To change transparency of label in views
    - Hover over thumb tack in top left of view.
    - Select '>>' button.
    - Change percent opacity by changing value near eye icon: 0.0 (transparent) to 1.0 (opaque).

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)