# How to merge multiple segments at once

**URL:** <https://discourse.slicer.org/t/how-to-merge-multiple-segments-at-once/30449>\
**Category:** Support\
**Tags:** build, segmentation, python\
**Created:** [July 7, 2023, 11:26am UTC](https://discourse.slicer.org/t/how-to-merge-multiple-segments-at-once/30449 "2023-07-07T11:26:05Z")\
**Posts on this page:** 12\
**Page:** 1

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**Author:** ![Kitchen-Sinkk](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/kitchen-sinkk/32/66688_2.png) [@Kitchen-Sinkk](https://discourse.slicer.org/u/Kitchen-Sinkk)\
**Post date:** [July 7, 2023, 11:26am UTC](https://discourse.slicer.org/t/how-to-merge-multiple-segments-at-once/30449/1 "2023-07-07T11:26:05Z")

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![slicer1](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/8/0829fbfa2b13968d6d7d9b252b378739baae023c.jpeg)

 ![SLICERS](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/1/11215015765472f55927e53e7c81c3bf14b69b57.jpeg)  
as the images showed, I have mutiple segements. I can add them one by one through the “logic operators” functions. However, I like to merge or “add” them together at once. Are there any method to achieve this goal?

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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 8, 2023, 4:09am UTC](https://discourse.slicer.org/t/how-to-merge-multiple-segments-at-once/30449/2 "2023-07-08T04:09:05Z")

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I find that the easiest to merge many segments is:

- show all the segments that you want to add (hide those segments you don’t want to add)
- select “Logical operators” effect
- select “Operation” → “Fill”
- uncheck “Bypass masking”
- select “Masking” / “Editable area” → “Inside all visible segments”
- click “Apply”

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**Author:** ![Kitchen-Sinkk](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/kitchen-sinkk/32/66688_2.png) [@Kitchen-Sinkk](https://discourse.slicer.org/u/Kitchen-Sinkk)\
**Post date:** [July 12, 2023, 1:28am UTC](https://discourse.slicer.org/t/how-to-merge-multiple-segments-at-once/30449/3 "2023-07-12T01:28:45Z")

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It’s work! thank you very much!

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [July 12, 2023, 8:36am UTC](https://discourse.slicer.org/t/how-to-merge-multiple-segments-at-once/30449/4 "2023-07-12T08:36:51Z")

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As this is such an important feature it would be nice to have a special entry or preset in the “Operation” dropdown like “Merge visible segments” which automates that recipe

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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 12, 2023, 2:09pm UTC](https://discourse.slicer.org/t/how-to-merge-multiple-segments-at-once/30449/5 "2023-07-12T14:09:32Z")

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Would it be enough if the “Logical operators” effect allowed selection of multiple input segments?

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [July 12, 2023, 2:31pm UTC](https://discourse.slicer.org/t/how-to-merge-multiple-segments-at-once/30449/6 "2023-07-12T14:31:24Z")

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Probably yes, maybe also “Fill/Merge”?

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**Author:** ![Deep\_Learning](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/deep_learning/32/15345_2.png) [@Deep\_Learning](https://discourse.slicer.org/u/Deep_Learning)\
**Post date:** [October 2, 2023, 3:47pm UTC](https://discourse.slicer.org/t/how-to-merge-multiple-segments-at-once/30449/7 "2023-10-02T15:47:11Z")

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Could you please clarify.  
I want to merge 4 segments.

Make the four segments visible.

- select “Logical operators” effect
- select “Operation” → “Fill”
- uncheck “Bypass masking”
- select “Masking” / “Editable area” → “Inside all visible segments”

%%%$$$ Now which segment should be selected before applying?

A new empty segment? Any one of the four segments…

No matter what I do, I end up with the whole volume segmented (A big box)

[  
lassoan](https://discourse.slicer.org/u/lassoan)[Andras Lasso](https://discourse.slicer.org/u/lassoan)

[Jul 8](https://discourse.slicer.org/t/how-to-merge-multiple-segments-at-once/30449/2)

I find that the easiest to merge many segments is:

- show all the segments that you want to add (hide those segments you don’t want to add)
- select “Logical operators” effect
- select “Operation” → “Fill”
- uncheck “Bypass masking”
- select “Masking” / “Editable area” → “Inside all visible segments”
- click “Apply”

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [October 3, 2023, 3:23pm UTC](https://discourse.slicer.org/t/how-to-merge-multiple-segments-at-once/30449/8 "2023-10-03T15:23:13Z")

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You should create a new segment → “combined”. Here is a short video showing the process:

[https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/7/87621985237ec8a8a2d30e9d65e0b200a4529169.mp4](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/7/87621985237ec8a8a2d30e9d65e0b200a4529169.mp4)

Good luck.

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**Author:** ![Deep\_Learning](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/deep_learning/32/15345_2.png) [@Deep\_Learning](https://discourse.slicer.org/u/Deep_Learning)\
**Post date:** [October 4, 2023, 12:02pm UTC](https://discourse.slicer.org/t/how-to-merge-multiple-segments-at-once/30449/9 "2023-10-04T12:02:31Z")

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[quote=“Deep\_Learning, post:7, topic:30449”]

Thank you, I was missing the “allow overlap”.

Slicer 5.1:

- show all the segments that you want to add (hide those segments you don’t want to add)
- select “Logical operators” effect
- select “Operation” → “Fill”
- create a new Segment and select it
- uncheck “Bypass masking”
- select “Masking” / “Editable area” → “Inside all visible segments”
- select “Modify other Segments”→ “Allow Overlap"
- click “Apply”

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**Author:** ![CS1](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cs1/32/80852_2.png) [@CS1](https://discourse.slicer.org/u/CS1)\
**Post date:** [November 14, 2025, 11:47am UTC](https://discourse.slicer.org/t/how-to-merge-multiple-segments-at-once/30449/10 "2025-11-14T11:47:04Z")

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Sorry lassoan, got a silly question, what happen with the overlapped volume/area between the two merged segments? would they be calculated twice Thanks!

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**Author:** ![cpinter](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cpinter/32/7995_2.png) [@cpinter](https://discourse.slicer.org/u/cpinter)\
**Post date:** [November 14, 2025, 11:48am UTC](https://discourse.slicer.org/t/how-to-merge-multiple-segments-at-once/30449/11 "2025-11-14T11:48:53Z")

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No, the merged segment will have no knowledge about where the different regions came from. Any statistic about the merged segment will be strictly about the contained voxel data in the segment.

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**Author:** ![CS1](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cs1/32/80852_2.png) [@CS1](https://discourse.slicer.org/u/CS1)\
**Post date:** [November 18, 2025, 12:04pm UTC](https://discourse.slicer.org/t/how-to-merge-multiple-segments-at-once/30449/12 "2025-11-18T12:04:30Z")

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Thank you! this is very helpful!