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Target Outcome

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



  • ITK-SNAP. ITK-SNAP is a software application used to segment structures in 3D medical images (GPL license, see http://www.itksnap.org).

  • Slicer. Slicer is a free, open source software package for visualization and image analysis (BSD-style open source license, see http://www.slicer.org).

  • MITK. The Medical Imaging Interaction Toolkit (MITK) is a free open source software platform aimed at providing support for an efficient software-development of methods and applications dealing with medical images (BSD-style license, see http://www.mitk.org).

  • SimpleITK. SimpleITK is a simplified layer built on top of ITK to facilitate its use in rapid prototyping of image analysis that can be used in interpreted languages, e.g. Python, (Apache 2.0 License license, see http://www.simpleitk.org/).

  • Convert3D. C3D is a command-line tool for converting 3D images between common file formats, which also includes a growing list of commands for image manipulation, such as thresholding and resampling (GPL license, see http://www.itksnap.org/pmwiki/pmwiki.php?n=Downloads.C3D).

Previous Protocols

For more details, see Specifications/ExperimentationAnatomicalImaging.



Set(s) of MRI in NifTI format



Image/Data Input/Output Procedures

Load MRI data:

Load segmented label map image data (NifTI):

Save segmented label map (as NifTI):

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

Viewing Options

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

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

Segmentation Setup

Manual Segmentation

Grow-Cut Segmentation

Grow Cut Effect

Grow Cut Effect

Grow Cut Effect

Grow Cut Effect

Image Processing Procedures

Label Map Smoothing

Generate Triangulated Surface (STL) from Label Map

Tissue-Specific Procedures

Registration Markers

INPUT: general purpose MRI

Procedure for registration marker segmentation:

  1. Use level tracing effect (foreground label) to segment registration markers on various slices, in various orthogonal viewing planes.
  2. On slices which were segmented in the prior step, manually define the area surrounding the markers with a different color (background label)
  3. Apply the Grow Cut effect automatically segment the remaining regions of the registration marker (as described above).
  4. Remove the background label using the ChangeLabelEffect (as described in the Grow Cut procedure).

    • Manually segment to fill in the screw hole on spherical registration markers on femur and tibia.
    • Manually segment to fill in bubbles using 'art' to define outer spherical boundary.

LABELS: FMR-M, FMR-L, FMR-P, TBR-M, TBR-L, TBR-P, PTR-S, PTR-M, PTR-L (includes bone and relative marker location, e.g. FMR-M is comprised of FM for femur, R for registration marker, and -M for medial).

oks001, femur and tibia registration markers (posterior):

Registration Marker Segmentation


INPUT: cartilage MRI (sagittal)

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 cortical region defines the bone surface.

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

oks001, femur:

Femur Segmentation

oks001, tibia:

Tibia Segmentation

oks001, patella:

Patella Segmentation

oks001, fibula:

Fibula Segmentation


INPUT: cartilage MRI

Procedure for cartilage segmentation:

Cartilage segmentation should be informed by bone segmentation (i.e. use bone boundary to help define cartilage boundary).

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

oks001, femur cartilage:

Femur Cartilage Segmentation

oks001, patella cartilage:

Patella Cartilage Segmentation

oks001, medial tibia cartilage:

Tibia Cartilage (Medial) Segmentation

oks001, lateral tibia cartilage:

Tibia Cartilage (Lateral) Segmentation


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. use cartilage boundary to help define meniscus boundary).

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

oks001, medial meniscus:

Meniscus (Medial) Segmentation

oks001, lateral meniscus:

Meniscus (Lateral) Segmentation

Connective Tissue - Ligaments & Tendons

Procedure for patellar ligament, quadriceps tendon, ACL, PCL (and any connective tissue when applicable):

Alternatively, one can display the ligament specific MRIs and the cartilage specific MRI in different windows. When linked, Slicer uses interpolation for coupled viewing of the image sets that are already spatially aligned. In return, one can do the segmentation on interpolated ligament MRIs using the cartilage MRI as the master volume for segmentation. This allows high resolution segmentation volume from images with lower resolution directly.

Procedure for LCL, etc.:

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

Connective tissue segmentation should be informed by bone segmentation (i.e. use bone boundary to help define connective tissue boundary).


oks001, patellar ligament:

Patellar Ligament Segmentation

oks001, quadriceps tendon:

Quadriceps Tendon Segmentation

oks001, ACL:

Anterior Cruciate Ligament Segmentation

oks001, PCL:

Posterior Cruciate Ligament Segmentation

oks001, LCL:

Lateral Collateral Ligament Segmentation

Sample Results


3D Reconstruction

3D Reconstruction

3D Reconstruction

3D Reconstruction

3D Reconstruction

3D Reconstruction

3D Reconstruction

3D Reconstruction