# Segment Editor functions don't work past specific slice in DICOM series

**URL:** <https://discourse.slicer.org/t/segment-editor-functions-dont-work-past-specific-slice-in-dicom-series/12839>\
**Category:** Support\
**Tags:** segmentation, dicom\
**Created:** [August 3, 2020, 10:09pm UTC](https://discourse.slicer.org/t/segment-editor-functions-dont-work-past-specific-slice-in-dicom-series/12839 "2020-08-03T22:09:02Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Otoco](https://avatars.discourse-cdn.com/v4/letter/o/b4bc9f/32.png) [@Otoco](https://discourse.slicer.org/u/Otoco)\
**Post date:** [August 3, 2020, 10:09pm UTC](https://discourse.slicer.org/t/segment-editor-functions-dont-work-past-specific-slice-in-dicom-series/12839/1 "2020-08-03T22:09:02Z")

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Hello all,

I’ve been spending the last few weeks segmenting skull bones using CT skull DICOMs for research purposes. I got a fantastic solution with the help of the users of this forum last time - my current problem is a little bit simpler.

On this specific DICOM series, when I use the segment editor the functions stop working after a specific image in the axial series. Threshold indicates that it wants to fill in the entire series but when I run the function, it is only partially filled. Manually painting the volume at any image in the unresponsive section doesn’t work either. I have no annotations currently active and never cropped the volume to begin with. Couldn’t find a thread with an equivalent problem after searching, so posting it here.

Screens:

 ![Screen Shot 2020-08-03 at 6.01.12 PM](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/a/a/aa1b52d261a0cf5384cc67b9a4c3ae8759e0ec91.jpeg)  
Here you can see that the threshold I did stopped at a specific axial slice.

 ![Screen Shot 2020-08-03 at 6.01.51 PM](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/4/54d5782f995d379070c1cc2647a04053499cc5a1.jpeg)  
This is the preview when I am applying a threshold to my segment - you can clearly see the problematic sections are included and this is true for the entire series.

 ![Screen Shot 2020-08-03 at 6.02.45 PM](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/5/f52012f4d78db5bf958287ee1a426a98c16d5144.jpeg)  
My attempt at painting above the problematic slice - didn’t change anything.

 ![Screen Shot 2020-08-03 at 6.06.06 PM](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/6/d63985315d2decd2c4d2ff1bc1d043b7bb558fda.png)  
Volume information if this helps - it’s a solid volumetric scan but not anything out of the ordinary.

Any help would be appreciated! Thank you all so much.

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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:** [August 3, 2020, 10:22pm UTC](https://discourse.slicer.org/t/segment-editor-functions-dont-work-past-specific-slice-in-dicom-series/12839/2 "2020-08-03T22:22:17Z")

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You can only paint within the extent of the “binary labelmap representation”. You can specify a larger extent by selecting a different node (e.g., the volume that contains the complete skull) and use it as source geometry (see some more information [here](https://slicer.readthedocs.io/en/latest/user_guide/modules/segmenteditor.html#panels-and-their-use)).

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [August 3, 2020, 10:25pm UTC](https://discourse.slicer.org/t/segment-editor-functions-dont-work-past-specific-slice-in-dicom-series/12839/3 "2020-08-03T22:25:43Z")

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You probably have the same issue as this thread:

> [@Uneven slice thickness](https://discourse.slicer.org/t/uneven-slice-thickness/6442):
>
> Any Solution for this?? [image]

See this info: [Documentation/Nightly/FAQ/DICOM - Slicer Wiki](https://www.slicer.org/wiki/Documentation/Nightly/FAQ/DICOM#Image_is_stretched_or_compressed_along_one_axis)

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<div class="post-metadata">

**Author:** ![Otoco](https://avatars.discourse-cdn.com/v4/letter/o/b4bc9f/32.png) [@Otoco](https://discourse.slicer.org/u/Otoco)\
**Post date:** [August 4, 2020, 5:14pm UTC](https://discourse.slicer.org/t/segment-editor-functions-dont-work-past-specific-slice-in-dicom-series/12839/4 "2020-08-04T17:14:56Z")

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this was the one! the node somehow was switched to a smaller view, redefining the source geometry fixed it. Thank you so much!