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.
-
If anybody has suggestions to improve the segmentation quality of cerebral arteries, please do not hesitate to post it here.
-
Sometimes the segmentation model is very big, then you can decrease the size in 3D Slicer.