# Automatic SWI venography segmentation using VMTK

**URL:** <https://discourse.slicer.org/t/automatic-swi-venography-segmentation-using-vmtk/29273>\
**Category:** VMTK\
**Tags:** segmentation\
**Created:** [May 3, 2023, 3:53pm UTC](https://discourse.slicer.org/t/automatic-swi-venography-segmentation-using-vmtk/29273 "2023-05-03T15:53:33Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![OVSofia](https://avatars.discourse-cdn.com/v4/letter/o/b782af/32.png) [@OVSofia](https://discourse.slicer.org/u/OVSofia)\
**Post date:** [May 3, 2023, 3:53pm UTC](https://discourse.slicer.org/t/automatic-swi-venography-segmentation-using-vmtk/29273/1 "2023-05-03T15:53:33Z")

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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 🙂

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [May 10, 2023, 4:35am UTC](https://discourse.slicer.org/t/automatic-swi-venography-segmentation-using-vmtk/29273/2 "2023-05-10T04:35:52Z")

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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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<div class="post-metadata">

**Author:** ![OVSofia](https://avatars.discourse-cdn.com/v4/letter/o/b782af/32.png) [@OVSofia](https://discourse.slicer.org/u/OVSofia)\
**Post date:** [May 22, 2023, 2:26pm UTC](https://discourse.slicer.org/t/automatic-swi-venography-segmentation-using-vmtk/29273/3 "2023-05-22T14:26:42Z")

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Thank you for your suggestions