Finding vessel diameter and tortuosity

[Demi]

Hi all, 

I am trying to calculate two different parameters of vessel segments without any bifurcations: the average diameter along the centerline of the vessel and the overall tortuosity, but it seems like I can not subtract this information directly from the data. For calculating the average diameter, I am running the following code:

vmtksurfacesubdivision -method loop -ifile E:/Testdata/testvessel2.stl -ofile testvessel2_edited.stl --pipe vmtksurfacereader -ifile testvessel2_edited.stl --pipe vmtkcenterlines -ifile testvessel2_edited.stl -ofile testvessel2_centerlines.stl --pipe vmtkrenderer --pipe vmtksurfaceviewer -opacity 0.25 --pipe vmtksurfaceviewer -i @vmtkcenterlines.o -array MaximumInscribedSphereRadius --pipe vmtkdistancetocenterlines -useradius 1 -ofile testvessel2_radius.vtp --pipe vmtksurfacewriter -f pointdata -ofile E:/Testdata/testvessel2_radius2.txt

This returns a txt file containing the parameters MaximumInscribedSphereRadius and DistanceToCenterline. It seems to me that the DistanceToCenterline is not calculated correctly, since it differs a lot from MaximumInscribedSphereRadius. Anyway, I would actually like to calculate the average diameter of the vessel along the centerline, instead of the minimum radius. Is this possible? And which function should I use? To find the tortuosity, I am running the following code:

vmtkcenterlinegeometry -ifile E:/Testdata/testvessel2_edited.stl -smoothing 1 -iterations 100 -factor 0.1 --pipe vmtksurfacewriter -i @.o -celldata 1 -ofile E:/Testdata/curveinfo2.dat

But this returns all zero values. I already tried to upload the file in Paraview, but there it also says the tortuosity is zero, which could not be true. What can I do to derive the diameter and the tortuosity from my data? 

Thanks in advance!

Demi 

[andra...@gmail.com]

I don’t use pypes scripts but these are fairly straightforward to compute using VMTK filters.

 

You can also use 3D Slicer’s SlicerVMTK extension to get average radius and tortuosity for your vessel segment. See https://github.com/vmtk/SlicerExtension-VMTK#the-vmtk-extension-for-3d-slicer for details.

 

Andras

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[Demi]

Hi Andras, 

Thanks for your fast advice. I downloaded 3D Slicer and managed to upload my vessel segment (a *stl surface file) and its centerline (a *vtk file) that I computed in VMTK. I opened the 3D table to find the averaged radius and the tortuosity, but the table was empty. What did I do wrong? Should I link the centerline to its vessel in some sort of way or does 3D Slicer automatically understand this? I added some screenshots including the errors just to make sure you can understand what I am talking about. Thanks!

Demi 

Op dinsdag 4 augustus 2020 22:12:56 UTC+2 schreef andra...@gmail.com:

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[Andras Lasso]

There is no need for the centerline, just load the surface mesh and let the Extract centerline module compute the centerline and metrics. 

Andras

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From: Demi
Sent: Friday, August 7, 2020 5:48 PM
To: vmtk-users
Subject: Re: [vmtk-users] Finding vessel diameter and tortuosity

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[Demi]

Hi Andras, 

Thanks again for the quick response. I tried to find that function earlier, but it seems like that module is not present, at least in my version of 3D Slice (see printscreen). I downloaded the latest stable version (4.10.2) of 3D Slicer. Should I try to download another version? Or is this function hidden under another module? Thanks!

Demi 

Op zaterdag 8 augustus 2020 02:08:00 UTC+2 schreef Andras Lasso:

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[Andras Lasso]

You need to use a recent Slicer Preview Release.

Andras

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From: Demi
Sent: Saturday, August 8, 2020 7:08 AM

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[Demi]

Hi Andras, 

I just installed version 4.11.0 on my Macbook, since it wouldn't install on my Windows computer, but I don't see any centerline modules when I type this in at the search bar. Where can I find this function? 

Best, Demi 

Op zaterdag 8 augustus 2020 14:54:18 UTC+2 schreef Andras Lasso:

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[Andras Lasso]

You need to install SlicerVMTK extension from extension manager. It provides "Extract centerline" module and others. 

Andras

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From: Demi
Sent: Saturday, August 8, 2020 9:01 AM

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[Demi]

Hi Andras, 

Thanks for clearing that up! I got it figured out now. 

Best, Demi 

Op zaterdag 8 augustus 2020 16:01:27 UTC+2 schreef Andras Lasso:

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