How to segment multiple vertebrae in spine CT for 3D printing

Step by step tutorial for segmentation a section of the lumbar spine and exporting it for 3D printing. Printed vertebrae can be inserted into commercial training phantoms for skill development and assessment on challenging, realistic training cases.
Download data set, slides, and more segmentation tutorials: www.slicer.org/wiki/Documenta...
Software used: 3D Slicer. Freely available at www.slicer.org.
Tutorial created by Hilary Lia, with help from Csaba Pinter, Andras Lass, and Tamas Ungi (PerkLab, Queen's University).

[@beeflavoramenoodles3527]

Great video. I also appreciate how you explain why you do each step.

[@JohnPamperin]

Excellent tutorial. Thank you so much!

[@JaswantSingh-lc7hq]

Excellent tutorial. Thank you for creating and sharing the video!

[@Muuip]

Great concise presentation! Great purpose! 👍

[@petetheweet]

Thank you so much for this, I've been struggling for days but I finally have an stl of my brain thanks to your video!

[@hareboll]

Great stuff!

[@michaellowry1888]

This is an amazing help, I have used some sample datasets in here and followed along, and was able to get some models here for 3d printing and this will be a valuable tool going forward for my work and research. Thanks again!

[@PerkLabResearch]

Check out additional documentation and tutorials at slicer.readthedocs.io/en/latest/user_guide/image_segmentation.html

[@crispy1315]

Thank you for uploading this video

[@user-pw2uu7zo5b]

Thanks! Very interesting experience

[@arjunbangalore6236]

Wonderful tutorial. I would like to use the data that you have used to practice. Is there a way that I can download data and the cylinder and holder model files?

[@AndrasLasso]

All data sets that were used in the tutorial are available here: www.slicer.org/wiki/Documentation/Nightly/Training#Slicer4_Image_Segmentation

[@m_atef144]

Hi, thanks for the tutorial. Is there a way to measure the cropped part dimensions?

[@ungitamas]

Yes, there is a ruler tool in Slicer. You find it in a drop-down menu next to the fiducial selector mouse mode button that looks like a blue arrow pointing up from a red ball (on the toolbar). Rulers can be placed by clicking at two different points in any viewer. You can drag the ruler end points to adjust them.

[@AndrasLasso]

You can also use Segment Statistics module to get surface, volume, min/man/mean image intensity, etc. for each segment.

[@NGSchmit]

How would you isolate the clavicle from the rest of the bones? I don't think I can use the scissor tool as it's not really in one of the three cardinal planes

[@PerkLabResearch]

You can use "Grow from seeds" effect - see for example here: kzbin.info/www/bejne/bn_FmmR5pJelnrs

[@andyadamovics855]

Thanks for the info! I'm new to this slicing software and could use a little help. I don't need to edit my dicom files like in the video but I am having some trouble converting to .stl properly. I am able to save what appears to be the correct .stl file to my computer but can't open it in any other slicing, preview or editing software. I followed the steps in the video but am having some trouble, can any one give me a hand? Thank you you very much, Andy

[@PerkLabResearch]

From this much information it is hard to tell what can be wrong. Use "Export to file" feature in Segmentations module. If you have problems opening the STL file in MeshLab then report the issue at the Slicer forum - discourse.slicer.org.

[@andyadamovics855]

@@PerkLabResearch Thanks for the help

[@Eddiezerintube]

THIS version available in slicer.kitware.com/midas3/item/297192

[@astronotusx]

Hi, what program did you use to create the cylinder? I tried to make one in Prusa Slicer and import it into 3D Slicer, but it does not work. Is there a possibility to create basic shapes and simple objects in the 3d Slicer itself? Thanks!

[@AndrasLasso]

Your can create models of simple shapes in "Create Models" module (in SlicerIGT extension). You can also create many other shapes using a few lines of Python script (using VTK library, as shown in examples in the Slicer Script Repository).

[@benjaminsoares4968]

Awesome! Where can I obtain the CT used? Thank you for this wonderful tutorial.

[@AndrasLasso]

I don't think we can share that specific image, but you can download similar CT scans in 3D Slicer's Sample Data module and many more at www.embodi3d.com/ and www.cancerimagingarchive.net/

[@aster4250]

I have a doubt, I have CT scan files with images in only one plane. And I have multiple CT scan files for the same patients. But because all the planes are not in one file, I cannot segment them. Is it possible to combine them into a single file?

[@PerkLabResearch]

This sounds like a regular DICOM image. You can load these using 3D Slicer's DICOM module: slicer.readthedocs.io/en/latest/user_guide/modules/dicom.html If you need further help then write to the Slicer forum at discourse.slicer.org

[@aster4250]

@@PerkLabResearch yes I got it. I was doing it wrong. I needed to load the whole directory I guess.

[@haggleshaggle]

Were any supports necessary?

[@ungitamas]

Yes, a lot.