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 usingThreshold
effect. - Remove remaining artifacts using
Islands
effect’sKeep 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
andCTABrainContrast
volumes (get the images using the links below). Significant patient motion is visible. To minimize artifacts, we need to align the images before subtraction.
- Go to
General registration (Elastix)
module - For
Fixed volume
choose baseline (no-contrast) volume - For
Moving volume
choose contrast volume as - For
Preset
choosegeneric (all)
- For
Output volume
, chooseCreate new Volume as...
and typeCTABrainContastAligned
- Click
Apply
and wait until the registration completes (it may take several minutes)
- Go to
Subtract scalar volumes
module to subtract baseline image from contrast image - For
Input volume 1
chooseCTABrainContrastAligned
- For
Input volume 2
chooseCTABrainBaseline
- For
Output volume
, chooseCreate new Volume as...
and typeCTABrainSubtracted
- Click
Apply
- Go to
Vesselness filtering
module - For
Input volume
chooseCTABrainSubtracted
- For
Seed point
chooseCreate 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.
- 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 increasingSuppress 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%).
- 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). ClickPreview
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. SetThreshold
toOff
.
- Go to
Segment editor
module. - Click
Add
button to create a new segment. - Double-click on the green rectangle in the
Color
column, start typingArtery
and hitEnter
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
.
- Visualize the results in 3D: Uncheck
Surface smoothing
in dropdown menu ofShow 3D
button to make 3D display update faster and prevent shrinking of vessels. Then clickShow 3D button
to see the vessels in the 3D view.
- To remove disconnected, non-vascular structures, click
Islands
effect, use the defaultKeep largest island
option, and clickApply
.
Final result with threshold = 0.07:
Final result with threshold = 0.15: