The first step in generating a geometry is importing the image data CRIMSON can handle [...] datatypes. Load the image data:
First, select the image data in the data manager. Then, go to "CRIMSON Geometry Modeling" and select "Vessel Path Editing". The "Vessel Path Editing" window will open on the right hand side of the GUI and you can add a "Vessel Tree" followed by a "Vessel Path". To start adding path points, click the "Edit" button. See these instructions in the image below:
To add points, hold control and click the left mouse button. To remove points, hold shift and click the left mouse button. The pointer will change as shown in the table below:
||Hold ctrl & click left mouse button|
||Hold shift & click left mouse button|
This is also demonstrated in the video below:
Using the Vessel Reslice Window¶
The vessel reslice menu allows you to move along the centerline of the vessel while adding or editing points. It will appear once you have added at least two points to the centerline.
This window contains a cross-sectional view along (perpendicular to) the centerline. The left is the re-sliced view using the original image and the right hand side is the gradient of the image. This view can be helpful when defining contours, since the gradient of the image will show the boundary of the lumen more clearly.
Note: vessel centerlines may also be imported into CRIMSON. This is done by right clicking on the vessel tree in the Data Manager and then clicking the Import Vessels button. These imported vessels must be in the VTK file format.
Vessel Segmentation - Manual¶
Once a vessel centerline is defined, the boundaries of the vessel are defined by adding contours. The Vessel Reslice window provides a re-mapped view of the vessel along the centerline so that accurate contours can be defined.
Click and hold the left mouse button to add a contour. The pointer will show which type of contour you are adding.
||Click & hold left mouse button|
Typically, circles are used in manual segmentation to generate the best possible solid geometry. However, ellipses and polygon contours can be helpful in unique patient geometries.
Similar to the points used to define the centerline, contours should be placed frequently enough along the centerline to fully capture the curvature and changing dimensions of the vessel while not too close to overfit or produce solid geometry generation artifacts.
One should also be mindful in tight vessel curvature, ensuring that contours do not overlap or intersect.
Using the vessel contours, loft the vessel into a 3D solid model.
The lofting algorithm may be changed between loft and sweep. For more information, see the advanced meshing page.
Vessel Segmentation - Auto¶
CRIMSON includes automatic vessel segmentation via the Region Growing algorithm.
|Begin region growing||Click & hold left mouse button|
|Grow region||Move mouse up (while holding)|
|Shrink region||Move mouse down (while holding)|
|Finish region growing||Release left mouse button|
After growing the region, you can switch back to a regular contour shape and edit the boundaries of the contours as shown at the end of this video:
Adding Vessel Branches¶
More vessels may be added to the tree by adding a "Vessel Path".
Note that the contours of a branching vessel should start completely within the parent branch. Contours extending beyond the parent wall will cause errors.
To generate a single solid geomeetry, vessels are blended. There are a few different algorithms available, but the most common is the fillet:
In CRIMSON the branches can be blended using the "Vessel Blending" window: