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Overview

  • Task: Segment cerebral vasculature on contrast-enhanced CT by background subtraction.
  • Imaging modality: any, with baseline (non-contrasted) and contrasted images available.

Prerequisites

  • SlicerElastix and SlicerVMTK extensions are installed.
  • Slicer-4.10 or later.

Recommended workflow

  • Align baseline (non-contrast) CT and contrast-enhanced CT using General registration (Elastix) module to minimize artifacts due to patient motion.
  • Subtract the baseline volume from contrast-enhanced volume using Subtract scalar volumes module.
  • Use Vesselness filtering module to remove non-vessel shaped structures (bone plates that have not been fully suppressed by subtraction).
  • In Segment editor module, use vesselness filtered image as master volume and extract vessels using Threshold effect.
  • Remove remaining artifacts using Islands effect's Keep largest island method.
  • Optionally compute vessel centerline using Centerline extraction module.

Tips:

  • If there is only rigid patient motion between baseline and contrast images then generic rigid (all) registration preset may be used, which attempts to align the images by applying rigid transform. It may be more robust and faster than using a warping transform.
  • Find a module by hitting Ctrl + F and start typing its name
  • Adjust window/level of the image to improve visibility of vessels in slice viewers: click Window/Level mouse mode in the toolbar and Ctrl + Left-click-and-drag with the mouse (starting from a vessel point) to set optimal window/level automatically.

Example

  • Load CTABrainBaseline and CTABrainContrast volumes (get the images using the links below). Significant patient motion is visible. To minimize artifacts, we need to align the images before subtraction.
    • CTABrainBaseline: download from here and rename the file to CTABrainBaseline.nrrd
    • CTABrainContrast: download from here and rename the file to CTABrainContrast.nrrd

Fading between baseline and contrast images. Significant patient motion is visible.

  • Go to General registration (Elastix) module
  • For Fixed volume choose baseline (no-contrast) volume
  • For Moving volume choose contrast volume as
  • For Preset choose generic (all)
  • For Output volume, choose Create new Volume as... and type CTABrainContastAligned
  • Click Apply and wait until the registration completes (it may take several minutes)

Fading between baseline and aligned contrast images. Patient motion is reduced.

  • Go to Subtract scalar volumes module to subtract baseline image from contrast image
  • For Input volume 1 choose CTABrainContrastAligned
  • For Input volume 2 choose CTABrainBaseline
  • For Output volume, choose Create new Volume as... and type CTABrainSubtracted
  • Click Apply

Subtraction image

  • Go to Vesselness filtering module
  • For Input volume choose CTABrainSubtracted
  • For Seed point choose Create new MarkupsFiducial and click in a vessel point in the image. Tip: Choose a point that is not trivial to segment, for example one that is near bone surfaces that are not fully suppressed by the subtraction.
  • Click Preview, wait for the filter preview to complete.

Vesselness filtering preview - with default parameters

  • Zoom out the slice views and inspect the results: some parts of the bone is detected as vessel. Increase suppression of plate-like structures by opening Advanced section and increasing Suppress plates value to 35% (other values that are used in this example: Minimum vessel diameter = 1 voxels, Maximum vessel diameter = 5 voxels, Vessel contrast = 52, Suppress blobs = 10%).

Vesselness filtering preview - with increased plate suppression

  • Optional: Check filtering results at a few different locations by deleting current point, then placing a new point in the slice viewer (click the trashcan icon next to Seed point, click the arrow button next to it, and click in the image). Click Preview button to see filtering results.

  • Click Start to perform vesselness filtering on the entire image. The operation may take a few minutes.

  • Optional: Adjust visualization of vesselness image in Volumes module. Set window (W) value to 1.0, set level (L) value to 0.5. Set Threshold to Off.

Vesselness filtering final result

  • Go to Segment editor module.
  • Click Add button to create a new segment.
  • Double-click on the green rectangle in the Color column, start typing Artery and hit Enter to accept the proposed name and color.
  • Select Threshold effect, set lower threshold value to 0.7 - to show the relevant vessels but still keep amount of artifacts under control. Click Apply.

Thresholding settings

  • Visualize the results in 3D: Uncheck Surface smoothing in dropdown menu of Show 3D button to make 3D display update faster and prevent shrinking of vessels. Then click Show 3D button to see the vessels in the 3D view.

Show 3D

  • To remove disconnected, non-vascular structures, click Islands effect, use the default Keep largest island option, and click Apply.

Final result with threshold = 0.07:

Animation of final result with threshold = 0.07.

Final result with threshold = 0.15:

Animation of final result with threshold = 0.15.