Scissors tool not working to remove unwanted areas 3D Slicer 4.9.0

Hi there,

I have been trying to segment a lower leg CT dataset and have been able to create a volume through importing the DICOM data --> volume rendering --> crop volume --> editor to chose the Bone (2) for the threshold affect–> Make model effect.

Having done all this the 3D image produced still has thing I want to remove - which I wanted to remove utilisng the scissor tool however, despite not changing any of the settings nothing seems to actually cut away. Would be great if someone could provide assistance to what I need to do/where I am going wrong.



Probably you export models to the scene and then use scissors effect to remove parts from the segmentation node, but of course the exported model nodes are not changed and still show those parts.

Do you actually use Model maker module? That is not necessary anymore if you use the Segment Editor, and it may be confusing to have static models generated by Model maker in the scene. Instead of using Model maker, it is better to only use the Show 3D button to see segmentation in 3D. When you are finished, you can use “Export to file” to write segmentation directly to 3D printable STL files.

If you still have problems using Scissors effect then let us know.

To remove small speckles, vessels, etc., it is more efficient to use Islands effect / Keep largest island method than remove manually using Scissors.

Hi Andras,

Thanks so much for your reply. I have tried to use the segment editor rather than using the model maker. However, it seems that the scissor and even the islands function are not working when I attempt to perform them.

With the scissors, I am outlining the area I want to use - however nothing will remove.

Are you suggesting that I keep the file as is and then save it as an STL file first, and then utilise the scissor function?

I am using a mac, not sure if that will affect anything in regards to the software.


Probably the best would be to learn a bit about how to use the Segment Editor by following these turorials:

They explain step by step how to use scissors and other effects.

Recent nightly versions contain direct export to file feature: Save segmentation directly to STL or OBJ files

Operating system does not matter: all features are available on Windows, Linux, and macOS.