# VMTK extension for PCA

**URL:** <https://discourse.slicer.org/t/vmtk-extension-for-pca/4497>\
**Category:** Support\
**Tags:** vmtk\
**Created:** [October 23, 2018, 10:43am UTC](https://discourse.slicer.org/t/vmtk-extension-for-pca/4497 "2018-10-23T10:43:38Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![14jwkn](https://avatars.discourse-cdn.com/v4/letter/1/57b2e6/32.png) [@14jwkn](https://discourse.slicer.org/u/14jwkn)\
**Post date:** [October 23, 2018, 10:43am UTC](https://discourse.slicer.org/t/vmtk-extension-for-pca/4497/1 "2018-10-23T10:43:38Z")

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Hello, I’m new to this and so far I’ve been using this tutorial ([https://na-mic.org/w/images/a/aa/VMTK\_Slicer\_3.6.3\_Updated\_OCT\_2011.pdf](https://na-mic.org/w/images/a/aa/VMTK_Slicer_3.6.3_Updated_OCT_2011.pdf)). I’ve been trying to do a segmentation for the PCA on a t1 divided by t2 MRI scan. I haven’t been able to get it to work, and I have a few questions.

1. What would be the optimal amount and optimal placement for the seeds for vesselness and level set segmentation?
2. When I do vesselness filtering, the preview displays the red parts filtered correctly but the output after the filtering is a black outline around the same parts. Is this an error and does it affect segmentation?
3. I read that the optimal settings for blood vessel segmentation include reducing blob-like structures threshold and increasing plate-like structures threshold. Are there other alterations I could do to troubleshoot?
4. Are there more resources where I could read about VMTK in Slicer specifically? The other tutorials I’ve read are about VMTK only.

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [October 23, 2018, 5:06pm UTC](https://discourse.slicer.org/t/vmtk-extension-for-pca/4497/2 "2018-10-23T17:06:13Z")

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You could have a look at the project writeup by @haehn [https://www.slicer.org/w/images/e/e8/Haehn-Slicer\_VMTK\_student\_research\_project.pdf](https://www.slicer.org/w/images/e/e8/Haehn-Slicer_VMTK_student_research_project.pdf)