Hi
My project is about computational fluid dynamic modeling of blood flow in an intracranial aneurysms. Can I extract the geometry from CT/Angio DICOM images in STL format in 3D Slicer?
And if the answer is yes, is the process of extracting looks like the other softwares like SimVascular?
Does the 3Dslicer employ machine learning to automatically generate the geometry or not?
Thank you in advance for your responses.
Yes, you can extract the cerebral vessels using plugin vesselness filter and local threshold and export the model in stl.
Thank you for your reply. Do you have any idea how can I find a tutorial related to my project? I have explored the instructions and tutorials, but I have found nothing useful so far.
I send you a private message.
Dear tsinesh,
could you also send me some references to the problem above?
I would really appreciate this.
Best Regards,
Marcin
Step-by-step manual for Segmentation of cerebral arteries in 3D Slicer
Install modul SegmentEditorExtraEffects.
Restart 3d Slicer and start segmenting.
Open a MRI file (e.g. Strg+o), “choose File to add” for 1 file.
If the MRI has a lot of inhomogenities use the “N4ITK MRI Bias correction” module (Ctrl+F for switch to modul search)
Select a input and output image, change settings in “advanced N4 parameter”, apply
I like to use also the LaplacianSharpeningImageFilter in the Modul “simple filter”
Extra detailed segmentation: If you really like to segment very small arteries, you should consider the use of module “vesselness filter” (you must add a “seeding point” inside an artery). Preview, adapt settings and Start. Later you can use “local threshold” method on this vesselnessFilterd image (details below) and add (using “logical operators”) the resulted segmentation to the normal segmentation (mean without vesselness filtered).
In the segment editor: “Add” a segment
Use method „Local threshold“
Change slider (blue arrow) to adapt intensity range of selected voxel (advice: low as possible, only few voxels should be outside the arteries), view the result in all slices (yellow arrow: go to all slices)
Minimum diameter: e.g. 0.5 mm (see blue arrow)
Important and not intuitive: select with the left mouse click one voxel inside a artery, press String + left click at the same time
Change view to 3D (activate Button “Show 3D” and change view option)
For cleaning (if to many wrong voxels were selected): use the “island” effect
Extra detailed segmentation: If you like to segment also smaller distal artery segments, you can add one more step: go to superior slices of the brain (blue arrow), activate Threshold (yellow arrow), decrease slider of “threshold range” as low as possible (only few voxels outside of arteries should be included), “Use for masking” ,
activate “Sphere brush” and increase diameter to 20% or 40%, paint the brain.
Remove the false-segmented voxels with the “island” effect, “keep largest island”, and adapt minimum size (e.g. 5000), apply in the end.
To export the segmentation (e.g. to stl), press the small arrow (below yellow arrow), export to file, choose folder, file format …
That’s it. I hope it help.
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If anybody has suggestions to improve the segmentation quality of cerebral arteries, please do not hesitate to post it here.
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Sometimes the segmentation model is very big, then you can decrease the size in 3D Slicer.
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when I imported the single bifurcated artery in Ansys fluent I wasn’t able to mesh the geometry for cfd analysis, how to solve the issue?