Table of contents:

Target Outcome

This specification targets at the 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

Infrastructure

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

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.
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.

Image/Data input procedures

Load MRI data:

• NifTi:

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

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

  • File -> DICOM (or click DCM icon button).

  • 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 (or click Data icon button).

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

• Select 'LabelMap' for all label map volumes.

• Click 'Ok'.

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

• Load segmented label map image as described above.
• From the “Modules” drop-down menu, select “Segment Editor”
• Check that the Master Volume is set as the desired MRI to be segmented.
• Load the label maps into the segment editor:
  • click “Segmentations”
  • scroll down and expand the “Export/Import models and label maps” tab
  • For “Operation”, select “Import”
  • Choose the desired label map from the “Input node” drop down.
  • Click “Import”

Image/Data output procedures

Exporting a label map from the Segment Editor module:

• If you are in the editing mode, click “Segmentations”
• Hide all segmentations besides the one that you wish to export using the eye toggle.
• Scroll down and expand the “Export/Import models and label maps” tab. For “Operation”, select “Export”
• From the “Output node” drop down, select the desired name. Note that this will override the existing label map with that name. If you wish, you may select “export to new labelmap” and then rename it as desired when saving.
• Expand the “Advanced” tab, and under “Exported Segments” drop down, select “Visible”.
• Click “Export”
• Save the label map using the directions below

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
• Click 'Save'

Save triangulated surface, STL (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
• Click 'Save'

Segmentation Procedures

Segmentation Setup

• From the "Modules" drop-down menu, select "Segment Editor"
• Under 'Master volume' select the desired MRI to be segmented (If no MRI is loaded, load using these directions). When multiple MRI sets are loaded, in most cases the desired MRI to be segmented should be the same as the Master Volume.
• Click "Add" to create a new segmentation. The name and color can be changed by clicking on them in the segmentation list.
• If the 'Effects' toolbar is not visible, select the segmentation in the list to highlight it, and then click "Edit selected".
• You are now ready to begin segmenting

Manual Segmentation

• Perform Segmentation Setup.
• Highlight the anatomy of interest in every slice, in each image plane orientation as appropriate (coronal, sagittal, axial).
• Different tools are available to highlight the anatomy of interest in the desired label color (e.g. label1):
  • Use the Paint Effect [with an appropriate/largest radius] to fill in the area using a brush.
  • Use the Draw Effect to draw the boundaries of the area - freehand or by right mouse click to set the polygon corners and left click to fill in the polygon.
  • Use the eraser to change the behavior of the tool, e.g. brush or pencil, to erase rather than draw.
• Tips and Shortcuts using 3DSlicer:
  • In Segment Editor Module:
    • 'z' to undo
    • 'y' to redo
    • arrow keys to move forward/background a slice

Grow-cut segmentation

• Perform Segmentation Setup
• Perform the following steps on roughly equally-spaced slices in each image plane orientation as appropriate (coronal, sagittal, axial). NOTE: If the borders are easily defined (ex: registration markers) then these steps only need to be performed on one or two slices in one image plane, plus cap the boundaries. If there is more ambiguity to the borders, perform the steps on 5-10 slices in one image plane, and just one or two in the others, plus cap the boundaries.
  • Use the Paint Effect [with an appropriate/largest radius] to highlight the anatomy of interest (foreground) using a specific label color.
  • Add another segmentation by clicking the "Add" button. Make sure it is a different color than the foreground label. Select the segmentation in the list to highlight it, whichever segmentation is highlighted is the one you are currently editing. Use the Paint Effect to highlight the area around the anatomy of interest (background).
• Export and Save the label maps just in case one of the following steps does not work as expected (or in case the program crashes).
• Select the "Grow from seeds" icon (under 'Effects')
• Click the "Initialize" button to view a preview of the grow cut segmentation
• Click the "Apply" button (Slicer window graphics will freeze until the grow cut algorithm is complete).
• Check the results. If you are not satisfied, click "Undo", and edit the segmentations more (ex: add more slices or more detail to slices). Repeat until results are satisfactory.
• Remove the background label by selecting if in the segmentation list, and clicking "Remove"
• See figures below for an example of segmentation using Grow Cut Segmentation with the foreground (green) and background (yellow).

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

Thresholding

• Perform Segmentation Setup.
• In effects, select the ‘Scissors’ tool
• Click ‘Masking’ and change the following parameters:
  • Editable area: Inside all visible segments
  • Editable intensity: click on the box and set the range from 0 to 100.
  • Overwrite other segments: None

Logical Operator

• Perform Segmentation Setup.
• In effects, select the ‘Logical operators’ tool
• In ‘Operation’ select the requested operation
• Click the ‘Apply’ button

Morphology

• Perform Segmentation Setup.
• In effects, select the ‘Smoothing’ tool
• In ‘Smoothing method’, select ‘Closing’
• Do not change Kernel size parameters
• Click the ‘Apply’ button

Grow

• Perform Segmentation Setup.
• In effects, select the ‘Smoothing’ tool
• In ‘Smoothing method’, select ‘Closing’
• Do not change Kernel size parameters
• Click the ‘Apply’ button

Joint Smoothing

• Import the desired label map to the segment editor.
• Select one of the label maps in the list, click “Edit Selected”
• Ensure that only the label maps you wish to perform joint smoothing on are visible. Hide all others using the eye toggle.
• Under “Effects” click “Smoothing”.
• In the “smoothing method” drop down select “Joint Smoothing”.
• Set the desired smoothing factor: try the default, and if it causes the label map to shrink too much, press undo, and repeat with a lower smoothing factor.
• Click “Apply”
• Check the results, and perform touchups as needed using the tools in "Effects".
• Once you are satisfied with the results, you must export the label maps from the segment editor module before saving (as NifTI).

Generate Triangulated Surface (STL) 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.
  • FOR RAW STL:
  • Under 'Model Maker Parameters', set 'Smooth' to zero.
  • Under 'Model Maker Parameters', set 'Decimate' 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.
• From Segment Editor:
  • If you are in the editing mode, click “Segmentations”
  • Hide all segmentations besides the one that you wish to export.
  • Scroll down and expand the “Export/Import models and label maps” tab. For “Operation”, select “Export”. For the “Output type” select “Models”.
  • From the “Output node” drop down, select the desired model hierarchy
  • NOTE: all models can be generated under the same or separate model hierarchies
  • Expand the “Advanced” tab, and under “Exported Segments” drop down, select “Visible”.
  • Click “Export”

Tissue-Specific Procedures

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

Bones

INPUT: cartilage MRI and general-purpose MRI

BOUNDARY DEFINITION: Cortical bone will appear in black in MRI 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. Click on ‘Add’ to create a new segment
4. Perform Logic Operator with the ‘Copy’ operation to duplicate the original segment.
5. Perform Thresholding to the duplicated segment to get the points outside the area of interest
6. Perform Logic Operator with the ‘Subtract’ operation to the original segment to remove the points outside the area of interest. In ‘Subtract segment’, select the duplicated segment
7. Perform Morphology to the original segment to fill the gaps inside the area of interest
8. Repeat the last 4 steps until the boundary is as desired
9. Perform Label Map Smoothing to remove noise

Go back to Overview for the next steps.

Ligament

INPUT: cartilage MRI

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

Procedure for ACL:

1. Load cartilage MRI.
2. Overlay previous ligament MRI segmented label map (from PHASE 1) over the cartilage MRI (as Foreground Layer, NOTE: make sure to increase opacity, default is 0). For more details see viewing options
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 boundaries as a guide.
5. Joint Smoothing between ligament and bones
6. Manual touch ups

Sample results

3D SURFACE REPRESENTATION OF SEGMENTED REGIONS

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)