# Segmentation leaves empty vertical lines

**URL:** <https://discourse.slicer.org/t/segmentation-leaves-empty-vertical-lines/2319>\
**Category:** Support\
**Created:** [March 14, 2018, 6:23pm UTC](https://discourse.slicer.org/t/segmentation-leaves-empty-vertical-lines/2319 "2018-03-14T18:23:21Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![alessandronavacchia](https://avatars.discourse-cdn.com/v4/letter/a/bc8723/32.png) [@alessandronavacchia](https://discourse.slicer.org/u/alessandronavacchia)\
**Post date:** [March 14, 2018, 6:23pm UTC](https://discourse.slicer.org/t/segmentation-leaves-empty-vertical-lines/2319/1 "2018-03-14T18:23:21Z")

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Hi all,

I am having trouble with segmenting an MRI. I am using the ‘draw’ tool in the ‘Segment editor’. I draw the outline you can see in this picture:

 ![draw_outline](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/9/595ecbbc2ef0ae8e183a3d0585fb48628f3fdba6.jpeg)

And when I press enter, this is what I get:

 ![draw_segmentation](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/a/5/a5e198c09781ea42449ddf7d4c6fb8d59a6bbe26.jpeg)

As you can see, there are unsegmented vertical lines that should be filled. In addition, some filled vertical lines show up in the next slice. I segmented one slice every three slices and this is what I get in the axial plane (see green lines on the left):

 ![axial](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/4/8437f6f438bb3f147a3ca8481ad984c606897d17.jpeg)

My guess is that this error is related to the orientation of the slices or something like that. Can someone help?

Thanks!

Alessandro

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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:** [March 14, 2018, 7:34pm UTC](https://discourse.slicer.org/t/segmentation-leaves-empty-vertical-lines/2319/2 "2018-03-14T19:34:13Z")

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Have a look at this topic, it should solve this for you:

> [@Segmentation Editor - How to disable painting on adjacent slices?](https://discourse.slicer.org/t/segmentation-editor-how-to-disable-painting-on-adjacent-slices/1459):
>
> I am working on a project where we are segmenting lesions from an MRI using the paint tool from the Segment Editor module. We are using a large brush size along with a threshold so only pixels within a certain range are included in the segmentation. My problem is that I want the segmentation to be only in 2d (i.e. just affecting the pixels on the current slice of the volume). For example, if I do a threshold paint on slice 10 of the MRI, I don’t want it to paint any of the pixels on slice 9 or …

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**Author:** ![alessandronavacchia](https://avatars.discourse-cdn.com/v4/letter/a/bc8723/32.png) [@alessandronavacchia](https://discourse.slicer.org/u/alessandronavacchia)\
**Post date:** [March 15, 2018, 2:22pm UTC](https://discourse.slicer.org/t/segmentation-leaves-empty-vertical-lines/2319/3 "2018-03-15T14:22:42Z")

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Steve,

that fixed the problem, thanks a lot for your help!

Alessandro