Hello,
Does anyone know how I could use VMTK to automatically segment vessels from SWI images? (particularly .nii format) I have been trying to get the vessel segmentation using vmtk (and vtk), but so far I can not do it automatically since have to give the range of the threshold. Is there a way to automatically get the values of the threshold for each image? And if not, is there any other method to get the segmentation automatically?
Thank you a lot 
You can use various segmentation tools in Segment Editor module. You can start with figuring out a good workflow for manual/semi-automatic segmentation tools and then automate it using Python scripting. Alternatively, you can segment a few hundred (but at least a few dozens) of cases and then train a fully automatic segmentation AI model using MONAILabel extension.
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Thank you for your suggestions