Manual Crop how to do it correctly

Operating system: win
Slicer version: 4.9

I’ve follow all instruction found here 3D Cropping Volume Rendering
If i’ve correctly understood, there is not a live crop direct on the main volume.

Then, i’ve make a segmentation - > exported to labelmap

then Open Mask scalar volume
Input MrBrainTumor (original volume)
Mask Volume: Segmentation label 1

Apply, the is ok

Now I go to volume rendering, I can display the main volume or the masked volume , but I see only a solid colored form (the mask selection) but not the tissue volume whit the volume rendering setting

Help please

Note that in recent version of Slicer, the workflow is much simpler than described in the old post, as Mask Volume effect allows masking directly from a segment, without leaving the Segment Editor module. Mask Volume will show up in the Segment Editor module after installing SegmentEditorExtraEffects extension.

See a short demo video here:


Fantastic thanks
It work good

And… does is possible to use simoultaneusly 2 separated mask for the same volume?

I don’t really understand what you mean by using separated masks. You can use all the tools in Segment Editor to draw shapes - they don’t have to be connected. You can also combine or separate a segments using Logical operators effect; or mask sequentially by using the same volume as Input volume and Output volume in Mask volume effect.

mmmm I cannot find how to make it
I’ve tried but dont work

I want try to use threshold AND Scissor, to isolate a little anatomic part and remove all little pixel outside…

Use Threshold effect first, then Scissors effect (erase outside), finally Islands effect (remove small islands).

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perfect, tested and work well many thanks

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Other little question, how to center the rotation center of 3D view on a specific point of 3D Volume: if I zoom very much, during rotation the volume go out of the window space

Click on the small box button (reset field of view) in the title bar of the 3D view to reset the center of rotation for the current content. I think Shift+LeftMouseDrag also shifts the center of rotation.

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A post was split to a new topic: Edit existing segmentation