Tutorial for doing Segmentation

Hello everybody,

I am working on creating annotated segmentation data for a project and a colleague recommended me to use 3D Slicer for the task.

I have installed 3D Slicer as well as its SlicerRT extension and have successfully loaded and visualized the segmentation for a data sample, which consists of multiple CT files and a RTSTRUCT.dcm file. Now I have to manually annotate other samples that I am given, and then export to corresponding RTSTRUCT.dcm files.

Could you please give me some advice on how I can get started with 3D Slicer for this task? Any references to tutorials/slides/videos are very much appreciated!

Thank you very much in advance for your help!


Thanks a lot! And sorry for the delay (I missed the notification email).

I would like to learn more about using Slicer to do 3D segmentation. Could you guys please point me to more references?

On the official page there are two tutorials listed:

  1. Segmentation for 3D printing: shows how to use the Segment Editor module for combining CAD designed parts with patient-specific models.
  1. Video tutorial: Whole heart segmentation from cardiac CT shows how to use the Segment Editor module for segmenting heart ventricles, atria, and great vessels from cardiac CT volumes.
  • Author: Andras Lasso, PhD
  • Audience: Users who need to segment heart structures, for example for visualization, quantification, or simulation.
  • Sample data set
  • Based on: 3D Slicer version 4.8

Unfortunately I don’t feel that they are enough for me :frowning:

I have found some additional tutorials on Google, e.g. [see my replies be low because I’m a new user so I cannot put more then 3 links] but they are for Slicer 3 :frowning: Could anybody with experience have a quick look and tell me if they are still relevant for Slicer 4?

Thank you so much in advance for your help!

Segmentation tutorials for Slicer 3 that I found:
https://www.slicer.org/w/images/8/80/OrbitSegmentationTutorial.pdf or http://www2.imm.dtu.dk/projects/BRATS2012/Jakab_TumorSegmentation_Manual.pdf

There are 3 step-by-step tutorials and several segmentation recipes on the training page of the latest Slicer version.

You can also find lots of questions and answers about segmentation on this forum (see segmentation tag or use the search function).

You may get help at any of the Slicer weekly hangouts or if you attend a Slicer project week.

If any of your questions are not answered, feel free to post it as a new topic in this forum.

There are a number of videos about performing certain segmentation tasks on this channel: