# New segment editor effects: Mask volume and Surface cut

**URL:** <https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699>\
**Category:** Support\
**Tags:** feature, segmentation\
**Created:** [July 17, 2017, 1:30pm UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699 "2017-07-17T13:30:09Z")\
**Posts on this page:** 18\
**Page:** 1

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [July 17, 2017, 1:30pm UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/1 "2017-07-17T13:30:09Z")

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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**.

Feedback and suggestions are welcome.

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**Author:** ![Fernando](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fernando/32/5640_2.png) [@Fernando](https://discourse.slicer.org/u/Fernando)\
**Post date:** [July 18, 2017, 8:56pm UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/2 "2017-07-18T20:56:04Z")

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They are awesome, thank you!

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**Author:** ![xackey](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/xackey/32/10860_2.png) [@xackey](https://discourse.slicer.org/u/xackey)\
**Post date:** [January 6, 2018, 5:40am UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/3 "2018-01-06T05:40:28Z")

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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?

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**Author:** ![xackey](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/xackey/32/10860_2.png) [@xackey](https://discourse.slicer.org/u/xackey)\
**Post date:** [January 6, 2018, 5:41am UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/4 "2018-01-06T05:41:03Z")

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![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/6/d61d4cb545999008b0e66a93a5a740a47beda5dc.jpeg)

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [January 6, 2018, 6:29am UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/5 "2018-01-06T06:29:04Z")

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Yes, the mask is somewhat smoothed, see more information in this [bug report](https://github.com/lassoan/SlicerSegmentEditorExtraEffects/issues/6). It is in easy fix, we just did not get to it yet, because the difference is so little that it is even hard to notice.

Is this causing significant error for you?  
Are you a developer, would you be interested trying to fix it?

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**Author:** ![xackey](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/xackey/32/10860_2.png) [@xackey](https://discourse.slicer.org/u/xackey)\
**Post date:** [January 6, 2018, 10:24am UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/6 "2018-01-06T10:24:55Z")

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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.

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**Author:** ![timeanddoctor](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/timeanddoctor/32/5839_2.png) [@timeanddoctor](https://discourse.slicer.org/u/timeanddoctor)\
**Post date:** [January 6, 2018, 10:47am UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/7 "2018-01-06T10:47:57Z")

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I have also confused by this bug. Thanks!

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [January 7, 2018, 3:58am UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/8 "2018-01-07T03:58:43Z")

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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.

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**Author:** ![Saima](https://avatars.discourse-cdn.com/v4/letter/s/9d8465/32.png) [@Saima](https://discourse.slicer.org/u/Saima)\
**Post date:** [January 23, 2020, 4:30am UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/9 "2020-01-23T04:30:29Z")

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Hi Andras,  
I am using surface cut but it do not make a surface rather it only makes a surface for only working slice. How it automatically selects all slices. is there any key to use with it.

Thank you

Regards,  
Saima Safdar

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [January 23, 2020, 11:24am UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/10 "2020-01-23T11:24:54Z")

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Scissors effect affect all slices. Do you mean that you would like to cut all _segments_ at once?

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<div class="post-metadata">

**Author:** ![Saima](https://avatars.discourse-cdn.com/v4/letter/s/9d8465/32.png) [@Saima](https://discourse.slicer.org/u/Saima)\
**Post date:** [January 24, 2020, 5:45am UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/11 "2020-01-24T05:45:03Z")

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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.

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**Author:** ![Saima](https://avatars.discourse-cdn.com/v4/letter/s/9d8465/32.png) [@Saima](https://discourse.slicer.org/u/Saima)\
**Post date:** [January 24, 2020, 6:46am UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/12 "2020-01-24T06:46:56Z")

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Thanks andras i figured out what i was doing wrong. the segment needs to be selected in red window and in greean and yellow as well. then it creates a surface in 3d.

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**Author:** ![Hasan\_Imanli](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/hasan_imanli/32/9697_2.png) [@Hasan\_Imanli](https://discourse.slicer.org/u/Hasan_Imanli)\
**Post date:** [January 29, 2021, 1:36pm UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/13 "2021-01-29T13:36:47Z")

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Hi Andras,

This seems to be very helpful tool, although it does not appear on my Slicer 3D (V 4.11.20200930, installed on Mac Pro macOS Big Sur).

Do you know how to fix it?

Thank you in advance

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/3/b/3bfeadfe73886f2d0b07863dd82ad26384b08ab8.jpeg)

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [January 29, 2021, 3:09pm UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/14 "2021-01-29T15:09:02Z")

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See above - these effects are provided by **SegmentEditorExtraEffects extension**.

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<div class="post-metadata">

**Author:** ![Hasan\_Imanli](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/hasan_imanli/32/9697_2.png) [@Hasan\_Imanli](https://discourse.slicer.org/u/Hasan_Imanli)\
**Post date:** [January 29, 2021, 4:33pm UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/15 "2021-01-29T16:33:51Z")

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Excellent, found it. Thank you so much

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**Author:** ![labakoum\_badr-eddine](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/labakoum_badr-eddine/32/17958_2.png) [@labakoum\_badr-eddine](https://discourse.slicer.org/u/labakoum_badr-eddine)\
**Post date:** [January 10, 2023, 12:14am UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/16 "2023-01-10T00:14:23Z")

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please what is the name of the surface cut model on the extension manager  
I have already installed the model Markups to model but I did not find in the segment editor part of the application

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [January 11, 2023, 4:13am UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/17 "2023-01-11T04:13:50Z")

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Surface cut effect will show up in Segment Editor module after you install SegmentEditorExtraEffects extension.

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<div class="post-metadata">

**Author:** ![labakoum\_badr-eddine](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/labakoum_badr-eddine/32/17958_2.png) [@labakoum\_badr-eddine](https://discourse.slicer.org/u/labakoum_badr-eddine)\
**Post date:** [January 12, 2023, 4:04pm UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699/18 "2023-01-12T16:04:32Z")

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yes it’s true I uninstalled it and I install it and it works very well