• Specifications
• ImageSegmentation

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TableOfContents()

Target Outcome

This specification targets at volumetric reconstruction of a tissue of interest, specifically the definition of the boundaries of the tissue,

• 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

Slicer

Overview

• Download desired image volume for the desired specimen (NifTI, .nii).
• Load the desired image volume into Slicer.
• Segment the tissue of interest using the detailed segmentation procedures described below.
  • NOTES:
  • Save the segmented label map regularly to avoid losing tedious work through program crashes. The file should be saved in the NifTI (.nii) format 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).
  • Segmented volume can be overlayed on other image sets to evaluate boundaries, however it can only be further edited when overlayed on MRIs with the same size/resolution as the MRI from which it was originally created.
• After completion of the segmentation, the volume should be exported as an image volume (NIFTI) and a triangulated surface (without smoothing) in STL format, e.g. oks001-fmb-01.stl

Image/Data Input/Output Procedures

Load MRI data:

• NifTI:

  • File -> Add Data (or Data icon button)

  • Click "Choose File(s) to add" button.
  • Select desired MRI(s) (.nii)
  • Click "Open".
• DICOM:

  • File -> DICOM, or click DCM icon.

  • Click "Import" button.
  • Select directory containing DICOM image slices (.IMA).
  • Click 'Add link'.
  • CLick 'OK' after images load.
  • Select desired Series in DICOM Browser window.
  • Click 'Load'.

Load segmented label map image data (NifTI):

• File -> Add Data

• Click 'Choose File(s) to Add'
• Select Segmented label map image(s) (NifTI, .nii)
• Click 'Open'
• Click/check 'Show Options'

• Click/check 'LabelMap'

  • NOTES:
  • Link 2D slice views in drop-down tack menu to ensure same label map is displayed in all views.
  • In Editor module, make sure 'Merge Volume' is set to label map if applying grow-cut or other editor methods.

Save segmented label map (as NifTI):

• File -> Save, or Save icon

• Deselect all modified/selected files in the 'File Name' field
• Select/Check the desired segmented label map volume (default type: NRRD, .nrrd)
• Set the 'File Format' to NifTI (.nii)
• Rename the label map volume as desired, see naming convention: ["Specifications/DataManagement"]
• Click 'Save'

Save triangulated surface (a.k.a. Slicer Model):

• File -> Save, or Save icon

• Deselect all modified/selected files in the 'File Name' field
• Select/Check the desired triangulated surface (default type: VTK, .vtk)
• Set the 'File Format' to STL (.stl)
• Rename the triangulated surface as desired, see naming convention: ["Specifications/DataManagement"]
• Click 'Save'

Viewing Options

Under the pin drop-down menu (under >> button) in any of the 2D slicer viewers:

• Link viewers to ensure that they all display the same label map volumes.
• Two label maps can be overlayed on the MRI in order to compare segmented boundaries between two different structures. The label map you want to edit should be set as the Label Layer (icon in pin drop-down 2D viewer menu with an "L"). The other label map can be loaded as the Foreground Layer (icon with an "F").
• Change transparency of the label map in 2D viewers by changing the percent opacity by changing value near the eye (display/hide) icon: 0.0 (transparent) to 1.0 (opaque).

Change contrast/brightness of MRI using the default mouse cursor pointer ( tool by clicking and dragging up/down and left/right in any of the 2D viewers.

Segmentation Procedures

Manual Segmentation

Insert Katie's instructions here!

Grow-Cut Segmentation

• From the "Modules" drop-down menu, select "Editor"
• If multiple MRI sets are loaded, make sure that the desired MRI to be segmented is selected as the Master Volume

• If it is the first time entering Editor Module, click Apply to select the default GenericAnatomyColors to create a new Merge Volume (i.e. label map, with the same size/resolution as the Master Volume)

  • If not the first time, make sure the desired label map overlayed (i.e. being edited) in the 2D slice viewers is the same as the Merge Volume.
• Perform the following steps on roughly equally-spaced slices in each image plane orientation as appropriate (coronal, sagittal, axial).
  • Use the Paint Effect (under 'Edit Selected Label Map' tab, top row of icons, 3rd icon from left) [with an appropriate/largest radius] to highlight anatomy of interest (foreground) using a specific label (e.g. label1).
  • Use the Paint Effect to highlight area around anatomy of interest (background) with a different label (e.g. label2).
  • Use the Paint Effect to "cap" boundaries of anatomy of interest (background) to prevent foreground leakage (before/after anatomy of interest appears).

• Select GrowCutEffect icon (under 'Edit Selected Label Map' tab, bottom row of icons, 3rd icon from left).

• Click the "Apply" button (Slicer window graphics will freeze until the grow cut algorithm is complete).
• Remove the background label:

  • Select ChangeLabelEffect (under 'Edit Selected Label Map' tab, bottom row of icons, 3rd icon from right).

  • Select label2 as input and background [0] as output.
  • Click the "Apply" button.

• See figures below for example of segmentation using GrowthCut Effect with foreground (green) and background (yellow).

attachment:gc1.png attachment:gc2.png attachment:gc3.png attachment:gc4.png

• For more information on Growth Cut Effect refer to the 3DSlicerWiki [http://www.slicer.org/slicerWiki/index.php/Modules:GrowCutSegmentation-Documentation-3.6].

• 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

Image Processing Procedures

Label Map Smoothing

• From the Modules drop-down menu, select 'Surface Models' -> 'Label Map Smoothing'

• Set Gaussian Smoothing Parameters, Sigma based on image resolution (e.g. 0.7 for cartilage MRI, resolution = 0.35 x 0.35 x 0.7 mm)
• From 'Input Volume' drop-down menu, select desired label map
• From 'Output Volume' drop-down menu, select 'Create and rename new Volume'
• Enter new name as desired, click 'OK'
• Click Apply

Generate Triangulated Surface from Label Map

• From the Modules drop-down menu, select 'Surface Models' -> 'Model Maker'

  • Under 'IO' tab, from 'Input Volume' drop-down menu, select desired Label Map
  • In Model drop-down menu, either 'Create and rename new Hierarchy' (e.g. default 'Models'), or select an existing Model Hierarchy.
    • NOTE: all models can be generated under the same or separate model hierarchies
  • Under 'Create Model' tab, specify a desired 'Model Name' for the select Label Map.
  • If no smoothing is desired, under 'Model Maker Parameters set 'Smooth' to zero.
  • Click Apply button.
• From Editor:

  • Select the MakeModelEffect

  • Set desired Label Map as the Merge Volume
  • If no smoothing is desired, deselect 'smooth model'
  • Click Apply button.

Tissue-Specific Procedures

Registration Markers

For Registration Marker segmentation, the following technique was used:

• Use the level tracing effect to fill in the registration markers in the beginning, middle, and end of it's respective appearances within the slices, for each view.
• Next fill in any gaps with the paint tool.
• Finally, on those slices, outline the area surrounding the markers with a different color and use the grow cut effect to fill in the segmentation (as described above).

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

INPUT: cartilage MRI

Procedure for bone segmentation:

1. Perform Grow Cut segmentation procedure on desired bone
2. Perform Label Map Smoothing to remove Grow Cut boundary noise
3. Perform manual segmentation to more accurately define bone boundary
4. Iteratively repeat last two steps until boundary is as desired NOTE: Cortical bone will appear black in MR images, so outer edge of black bone region defines the bone surface.

OUTPUT LABELS: FMB (femur), TBB (tibia), FBB (fibula), PTB (patella).

oks001, femur:

attachment:oks001_cMRI-femur_SEG.png

oks001, tibia:

attachment:oks001_cMRI-tibia_SEG.png

oks001, patella:

attachment:oks001_cMRI-patella_SEG.png

oks001, fibula:

attachment:oks001_cMRI-fibula_SEG.png

Cartilage

INPUT: cartilage MRI

Procedure for cartilage segmentation:

• Same as procedure for bone segmentation.

Cartilage segmentation should be informed by bone segmentation, i.e. subtraction of bone volume to trim back surface of cartilage.

OUTPUT LABELS: FMC (femoral), TBC-M (medial tibial), TBC-L (lateral tibial), PTC (patellar).

oks001, femur cartilage:

attachment:oks001_cMRI-femur_cartilage_SEG.png

oks001, patella cartilage:

attachment:oks001_cMRI-patella_cartilage_SEG.png

oks001, medial tibia cartilage:

attachment:oks001_cMRI-tibia_cartilage_MED_SEG.png

oks001, lateral tibia cartilage:

attachment:oks001_cMRI-tibia_cartilage_LAT_SEG.png

Menisci

INPUT: cartilage MRI

Procedure for menisci segmentation:

1. Manual segmentation
2. Label map smoothing
3. Manual touch-up

Menisci segmentation should be informed by cartilage segmentation, i.e. subtraction of menisci volume to match cartilage boundaries.

OUTPUT LABELS: MNS-M (medial), MNS-L (lateral).

oks001, medial meniscus:

attachment:oks001_cMRI-meniscus_MED_SEG.png

oks001, lateral meniscus:

attachment:oks001_cMRI-meniscus_LAT_SEG.png

Ligaments & Tendons

Procedure for patellar ligament, quadriceps tendon (and any other applicable tissue):

• PHASE 1 (INPUT: ligament MRI):
  1. Load sagittal ligament MRI.
  2. Perform the Grow Cut segmentation procedure on desired tissue.
  3. Modify the label map boundary manually if desired.
  PHASE 2 (INPUT: cartilage MRI):
  1. Load cartilage MRI.
  2. Overlay ligament MRI segmented label map over the cartilage MRI (as Foreground Layer).
  3. Create new label map (Merge Volume) from cartilage MRI (set as Label Layer).
  4. Manually segment the tissue using the ligament MRI label map bounaries as a guide.

Procedure for ACL, PCL, LCL, etc.:

1. Manual segmentation
2. Label map smoothing
3. Manual touch-up

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

OUTPUT LABELS: ACL, PCL, LCL, PTL, QAT, etc.

oks001, patellar ligament:

attachment:oks001_cMRI-patellar_ligament_SEG.png

oks001, quadriceps tendon:

attachment:oks001_cMRI-quad_tendon_SEG.png

oks001, ACL:

attachment:oks001_cMRI-ACL_SEG.png

oks001, PCL:

attachment:oks001_cMRI-PCL_SEG.png

oks001, LCL:

attachment:oks001_cMRI-LCL_SEG.png

3D SURFACE REPRESENTATION OF SEGMENTED REGIONS:

attachment:oks001_ALL_SEG_3D_A.png

attachment:oks001_ALL_SEG_3D_AM.png

attachment:oks001_ALL_SEG_3D_M.png

attachment:oks001_ALL_SEG_3D_MP.png

attachment:oks001_ALL_SEG_3D_P.png

attachment:oks001_ALL_SEG_3D_PL.png

attachment:oks001_ALL_SEG_3D_L.png

attachment:oks001_ALL_SEG_3D_LA.png

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)