Tutorial: Manipulate bifurcation

The goal with morphman-bifurcation is to control the angle between two daughter branches in a bifurcation, see Figure 1. The daughter branches can be rotated towards each other, in other words reduce \(\theta\), or towards the parent artery, increasing \(\theta\). The naming convention is that the largest daughter branch is numbered 1, and the smallest 2.

The algorithm builds on previous work of Ford et al. [1]

Figure 1: An illustration of the goal of morphman-bifurcation.

In this tutorial, we are using the model with ID C0005 from the Aneurisk database. For the commands below we assume that there is a file ./C0005/surface/model.vtp, relative to where you execute the command. Performing the manipulation can be achieved by running morphman-bifurcation in the terminal, followed by the respective command line arguments. Alternatively, you can execute the Python script directly, located in the morphman subfolder, by typing python manipulate_bifurcation.py. We have also created a demo folder where we show how to run this tutorial from a Python script, please check out the code from GitHub to run the demos.

Shown in Figure 2 is the result of rotating the two daughter branches with both a positive and negative angle.

Figure 2: Rotation of daughter branches, in both a widening and narrowing of the bifurcation angle.

You can reproduce the results in Figure 2 by running the following command:

morphman-bifurcation --ifile C0005/surface/model.vtp --ofile C0005/surface/rotate_plus.vtp --angle 20 --region-of-interest commandline --region-points 43.2 70.5 26.4 84.4 60.6 50.6 --poly-ball-size 250 250 250

for narrowing of the bifurcation angle, and similarly for widening of the bifurcation angle:

morphman-bifurcation --ifile C0005/surface/model.vtp --ofile C0005/surface/rotate_minus.vtp --angle -20 --region-of-interest commandline --region-points 43.2 70.5 26.4 84.4 60.6 50.6 --poly-ball-size 250 250 250

Inspecting Figure 2 closely you can observe an unphysiological “notch” in the bifurcation of the surface with increased \(\theta\). One remedy is to add the flag --bif True and --lower True, which will output a smoother bifurcation, as shown on the right side in Figure 3, compared with a model with no flags. The results shown in Figure 3 can reproduced by running the command:

morphman-bifurcation --ifile C0005/surface/model.vtp --ofile C0005/surface/rotate_no_notch.vtp --angle -20 --bif True --lower True --region-of-interest commandline --region-points 43.2 70.5 26.4 84.4 60.6 50.6 --poly-ball-size 250 250 250

Using both flags have proven to give an improved surface, and when used for computational fluid dynamics, a more physiological plausible wall shear stress [2].

Figure 3: Rotation of daughter branches with a different reconstruction of the bifurcation.

The default is to rotate both branches, but if either --keep-fixed-1 or --keep-fixed-2 is set to True, daughter branch 1 or 2 will be kept fixed, respectively. Furthermore, if both parameters are set to True then the algorithm can be used to remove an aneurysm (a balloon-shaped bleb on the artery), see Figure 4. To this specific tutorial, we have used the model with ID C0066 , which harbors an aneurysm located at the terminal bifurcation in the internal carotid artery.

Figure 4: Remove an aneurysm from the bifurcation.

To reproduce the result shown in Figure 4, you can run the following command:

morphman-bifurcation --ifile C0066/surface/model.vtp --ofile C0066/surface/removed_aneurysm.vtp --keep-fixed-1 True --keep-fixed-2 True --bif True --lower True --angle 0 --region-of-interest commandline --region-points 31.37 60.65 25.21 67.81 43.08 41.24 --poly-ball-size 250 250 250

For additional information, beyond this tutorial, on the script and input parameters, please run morphman-bifurcation -h or confer with the manipulate_bifurcation().

[1]	Ford, M.D., Hoi, Y., Piccinelli, M., Antiga, L. and Steinman, D.A., 2009. An objective approach to digital removal of saccular aneurysms: technique and applications. The British Journal of Radiology, 82(special_issue_1), pp.S55-S61.

[2]	Bergersen, A.W., Chnafa, C., Piccinelli, M., Gallo, C., Steinman, D.A., and Valen-Sendstad, K. In preparation. Automated and Objective Removal of Bifurcation Aneurysms: Incremental Improvements?