Scissors tool is awesome

The new segment editor in the 3D Slicer has features that the older Editor module lacks. One of this features is the awesome Scissors tool, which let’s you remove/retain any portion of the data by drawing an outline either in the slice views or in 3D.

Our goal in this tutorial will be to remove the foam and other support structures that usually show up in CT scans quickly (in about 2 minutes). We will use a dataset from the Terry Collection (TC 815) courtesy of Dr. Lynn Copes. For this tutorial I am using Slicer release r25914 (4.7.0-2017-04-10).

  • Download the nifti file and drag it into Slicer.
  • Go to the Segment Editor and create a new segment
  • Use the threshold tool with 410 – 4096 range to segment bones. Note that this picks up a fair amount of the scanning platform, as well as the foam.
  • If you want to visualize, you can click the create surface to see in 3D (takes a minute)

  • Switch to scissors tool and in the axial plane (red slice view) make a tracing of the scanning platform. Your scissors settings should be ‘erase inside’. This will remove the scanning platform from the segment #1, and assign it to the background.
  • Remaining foam particles can be easily dealt with using the Island tool. Just choose the option ‘Keep only the largest island‘.
  • You should have the skull fully segmented from the scanning platform and free of foam particles.

Segment editor uses a different data structure than regular editor. If you want to save a new dataset without the platform and the foam, you need to:

  1. Convert the segments into a label map. Right click on the Segment 1 and choose ‘convert visible segments to binary label map‘. For that, switch to Segmentations module, scroll down half to fine the tab Export/Import models and label maps. There you can specify to export the segmentation either as a label map or a surface model.  Note that there is an option to directly export a surface model as well, if that’s what you prefer to work with.
  2. To remove the platform, use the “Mask Scalar Volume” module, specify TC815 as your input volume, the label map from the previous step as your mask volume, and create a new output volume.

Edit on 9/25: There is now an extension that adds masking functionality to Segment Editor. It is called “slicer segment editor extra effects” and can be installed through the Extension Manager using a nightly (it isn’t available for the latest stable 4.6).  There is a video tutorial demonstrating the functionality.


You can use the scissors tool directly on the 3D view as well. Remember it is going to carve in (or carve out everything else depending your setting) into the screen plane, so orienting your specimen correctly is very important.

12 thoughts on “Scissors tool is awesome

  1. Jake

    When I try to use the scissor tool to cut out sections on the 3D model it doesn’t do anything. I have the suggested extensions and followed the video tutorial but it doesn’t seem to work.

    I tried using paint first then cutting over it but this only removes the painted section. Is it possible that my section is not including the 3D section? Do you have any idea how to address these issues?

    1. maga Post author

      Did you first create a segment that you visualized in 3D viewer? E.g. use the threshold effect to make a segment, then use the scissors tool.

  2. Thelma Looms

    Dr. Maga,

    I am following the steps in the tutorial but when I right-click on Segment_1 the message “Show only selected segments” appears. I am not given the option to create a label map or model. I am using version 4.7.0-2017-08-3 on Windows 10.

    Thank you for this tutorial!

    1. maga Post author

      Dear Thelma,
      That’s a mistake in the tutorial that I meant to correct but forgot. To export your segmentations (either as label or module), you can use the Segmentations module, and scroll down to the bottom of the tab.

  3. Ramón González

    Dear Dr.Murat Maga.
    Maybe you could help me. After importing from Morphosource a ply file into 3d slicer,could be modified with scissors tool or other tool?
    Thanks for your time.

    1. maga Post author

      Well, kind of. It has a lot of steps involved, and it is not guaranteed to work. You will probably be better of using a polygon editing tool like MeshLab. But if you insist on Slicer, you can try these steps:
      1. Load your ply/stl into Slicer
      2. Go to Segmentations module, create a new segmentation, scroll down and find the export/import segmentations, choose the operation as import and the input type as model, and then specify the input model hierarchy (whatever your morphosource ply is listed under models module. It should be a single item, if you loaded a single model)
      3. This will generate a segmentation, but that’s not enough. You need a volume that will go with this segmentation to be able to use the Segment Editor. Now change the export/import operation to export and specify the output node as label map, then hit export. Depending on the complexity of the model this may take a while.
      4. Now you got everything to use the Segment Editor (ie. a volume and a segmentation), set the master volume to the newly created labelmap (it may ask you to change from binary representation and may say something about accuracy). Now you should be able to use scissors (or other Segment Editor effects).
      5. To save your edits remember to export the final result as a new model (reverse of step #2) and save the model as ply or stl.

      Again, this is not what Slicer is intended for, but I confirmed these steps with the provided sample data (MRHead). Your mileage may vary other datasets.

  4. Ramón González.

    Dr.Murat Maga:Now, after cleaning with scissor tool,I can export the stl file for 3d printing.Thanks a lot¡

  5. Ramón González

    Dr Murat Maga:thanks for teaching scissors tool.I’m agree,it´s awesome.
    After cleaning,with scissor tool,I can´t save the stl/obj file for 3d printing.With regular editor,model maker tool allows save stl/obj file for 3d printing.Please,could you show me how to save,at the Segment Editor,an stl/obj file?
    Thank you very much.

    1. maga Post author

      Dear Ramon,

      After you are done with ‘Segment Editor’, you need to use the ‘Segmentations’ module to export your segmentation into a ‘Models’ module. From there you can save it as stl/ply.
      I will update the entry to reflect this more clearly.


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