Additional information can be found on the Discussion page.


Target Outcome

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

Prerequisites

Infrastructure

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

Previous Protocols

For more details, see Specifications/ExperimentationAnatomicalImaging.

Protocols

Input

Set(s) of MRI in NifTI format

Overview

  1. Download the image volume for the desired specimen (NifTI, .nii).
  2. Load the desired image volume into Slicer using these directions.

  3. Segment the tissue of interest using the detailed tissue specific segmentation procedures.

    • NOTES:
    • Save the segmented label map regularly to avoid losing tedious work through program crashes.
    • 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.
  4. After completion of the segmentation, the volume should be exported as an image volume (NIFTI) using these directions.

  5. Generate a triangulated surface from all segmented tissues (without smoothing) this is considered a RAW STL.

    • NOTE: Complete this step only after all tissue segmentations are completed, as it is common to make changes throughout the process.

How to navigate this page

If you are new to segmentation, it is recommended to first load an image into slicer, and read through the Viewing Options, Segmentation Procedures, and Image Processing Procedures sections to familiarize yourself with the program and the tools you will be using. Then, follow the directions in the Tissue Specific Procedures section, which will guide you through which segmentation procedures to use for each tissue type. Refer back to the detailed procedure descriptions as needed.

Image/Data Input Procedures

Load MRI data:

Load segmented label map image data (NifTI):

Importing a segmented label map to the "segment editor" module

Image/Data Output Procedures

Exporting a label map from the Segment Editor module:

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:

Segmentation Procedures

Several methods for segmentation in 3DSlicer are described here. The choice of method depends on the tissue type, and personal preference. Below, in tissue specific procedures, guidelines are provided for segmentation procedures based on tissue type.

Segmentation Setup

Manual Segmentation

For first time users, see https://www.slicer.org/wiki/Documentation/4.8/Modules/Editor for more information.

Grow-Cut Segmentation

Grow Cut Effect

Grow Cut Effect

Grow Cut Effect

Grow Cut Effect

Image Processing Procedures

Label Map Smoothing

Joint Smoothing

Joint smoothing is performed in the “Segment Editor” module

Generate Triangulated Surface (STL) from Label Map

Note: : In this stage a RAW STL is being created, therefore no smoothing procedures will be performed when generating the STL.

Once the STL has been generated, save it using these directions.

Tissue-Specific Procedures

Below are the guidelines for segmentation procedures based on tissue type.

Registration Markers

INPUT: general purpose MRI

Procedure for registration marker segmentation:

  1. Perform Grow Cut Segmentation procedure on desired marker.

  2. FOR SPHERICAL FEMUR/TIBIA MARKERS:
    • Manually Segment to fill in the screw hole on spherical registration markers on femur and tibia.

  3. IF MARKERS ARE PLASTIC SPHERES WITH ULTRASOUND GEL:
    • 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).

Go back to Overview for next steps.

oks001, femur and tibia registration markers (posterior):

Registration Marker Segmentation

Bones

INPUT: cartilage MRI (sagittal)

BOUNDARY DEFINITION: Cortical bone will appear black in MR images, so outer edge of black cortical region defines the bone surface.

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

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

Go back to Overview for next steps.

oks001, femur:

Femur Segmentation

oks001, tibia:

Tibia Segmentation

oks001, patella:

Patella Segmentation

oks001, fibula:

Fibula Segmentation

Cartilage

INPUT: cartilage MRI

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

Procedure for cartilage 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. Perform Joint Smoothing between cartilage and neighboring bone

  5. Perform manual touch up

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

Go back to Overview for next steps.

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

Menisci

INPUT: cartilage MRI

BOUNDARY DEFINITION: Menisci segmentation should be informed by cartilage segmentation (i.e. use cartilage boundary to help define meniscus boundary).

Procedure for menisci segmentation:

  1. Manual Segmentation

  2. Label Map Smoothing

  3. Manual touch-up
  4. Perform Joint Smoothing between meniscus and cartilage

  5. Manual touch-up

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

Go back to Overview for next steps.

oks001, medial meniscus:

Meniscus (Medial) Segmentation

oks001, lateral meniscus:

Meniscus (Lateral) Segmentation

Connective Tissue - Ligaments & Tendons

INPUT: ligament MRI (boundary definition), cartilage MRI(resolution)

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

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, MCL:

  1. Manual Segmentation

  2. Label Map Smoothing

  3. Manual touch-up

LABELS: ACL, PCL, LCL, MCL, PTL, QAT.

Go back to Overview for next steps.

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 SURFACE REPRESENTATION OF SEGMENTED REGIONS:

3D Reconstruction

3D Reconstruction

3D Reconstruction

3D Reconstruction

3D Reconstruction

3D Reconstruction

3D Reconstruction

3D Reconstruction

Output

Specifications/ImageSegmentation (last edited 2019-05-30 14:39:30 by klonowe)