See short demo video of the new “Mask volume” and “Surface cut” Segment editor effects here:
These effects were developed by Kyle Macneil (Med-i Lab, Queen’s University; SPL, Brigham and Women’s Hospital), with help from @lassoan and @fedorov . Thank you for your contribution!
Mask volume: Blanks out a segment or surrounding area in a volumetric image. Useful for quick removal of unwanted objects (such as CT table) or showing only a selected organ. It can also be used for creating a binary mask for registration, bias correction, etc. This effect essentially makes “Mask scalar volume” module functionality available conveniently in Segment editor.
Surface cut: Creates a surface from a set of points placed at the boundary of a structure in multiple views. The surface then can be used to create a segment or added or removed from an existing segment. The surface can be edited in slice and 3D views in real-time. Useful for quick approximate segmentation of structures with mostly convex shape. This effect essentially makes “Markups to model” module functionality available conveniently in Segment editor.
Available in latest nightly build in SegmentEditorExtraEffects extension.
Thank you for this nice tool!
But, I noticed that masked image and segmentation did not become same shape. They are slightly different shape as shown in the attached image below.
Is is bug?
Could you give me any suggestion?
Yes, I am very interested in fix.
I am Japanese radiologist in university hospital. I want to evaluate CT density histogram of lung nodule, but I don’t know how to do this by 3D slicer (Do you know this?).
So, as an alternative way, I want to analyze masked images using ImageJ software. But if masked images and segmentation are different, histogram will be different.
I’ve updated mask volume effect to use the segment’s binary labelmap representation instead of closed surface representation, so now it should work as you expected. The update is available if you reinstall Slicer or SegmentEditorExtraEffects extension on Jan 7 or later.
I want to select all segments using the surfacecut tool to have a surface but I am unable to do it as described in the video for surface cut for segmenting heart. the surface cut tool only selects the portion of segment using fiducials in the working slice.