# Vagina segmentation and reconstruction from MRI image

**URL:** <https://discourse.slicer.org/t/vagina-segmentation-and-reconstruction-from-mri-image/31989>\
**Category:** Support\
**Created:** [October 1, 2023, 11:24pm UTC](https://discourse.slicer.org/t/vagina-segmentation-and-reconstruction-from-mri-image/31989 "2023-10-01T23:24:20Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Miri\_Trope](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/miri_trope/32/67690_2.png) [@Miri\_Trope](https://discourse.slicer.org/u/Miri_Trope)\
**Post date:** [October 1, 2023, 11:24pm UTC](https://discourse.slicer.org/t/vagina-segmentation-and-reconstruction-from-mri-image/31989/1 "2023-10-01T23:24:20Z")

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Dear community,

I am currently in the process of segmenting the vagina from MRI images. I came across a research paper where they used OsiriX to delineate the vaginal contour (vagina\_sed\_1). I’m curious if Slicer, offers similar marking tools. If so, I’m interested in learning how to aggregate all those marked regions into a surface, similar to what was achieved in the paper (vagina\_sed\_2). Any guidance or assistance on this would be greatly appreciated.

Best regards,  
Miri

 ![vagina_seg_2](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/e/4e4d4502c03b2d0dfa1656084a5a7e8d7e6c93a6.png)  
 ![vagina_seg_1](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/c/8/c82a95bb85c806e23b9ecaa20232e74c4e7a4a52.png)

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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:** [October 1, 2023, 11:25pm UTC](https://discourse.slicer.org/t/vagina-segmentation-and-reconstruction-from-mri-image/31989/2 "2023-10-01T23:25:56Z")

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Slicer has much more extensive and sophisticated set of image segmentation tools compared to OsiriX. [This page](https://slicer.readthedocs.io/en/latest/user_guide/image_segmentation.html) is a good starting point to learn more.

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**Author:** ![Miri\_Trope](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/miri_trope/32/67690_2.png) [@Miri\_Trope](https://discourse.slicer.org/u/Miri_Trope)\
**Post date:** [October 2, 2023, 6:08am UTC](https://discourse.slicer.org/t/vagina-segmentation-and-reconstruction-from-mri-image/31989/3 "2023-10-02T06:08:42Z")

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Thank you for your response. To clarify further: I’m looking for a tool that can consolidate multiple “closed-curves” (marked with the Markups tool) into a single model, similar to the image I included in my initial message. A similar question regarding regions marked manually with the paint tool. Let’s say I have multiple painted circles that collectively form a tube-like structure (with gaps between the slices). How can I combine all of these segmented circles into a single model within Slicer?

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**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [October 2, 2023, 8:04am UTC](https://discourse.slicer.org/t/vagina-segmentation-and-reconstruction-from-mri-image/31989/4 "2023-10-02T08:04:57Z")

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> [@Miri\_Trope](#):
>
> aggregate all those marked regions

Instead of marking as in the picture, you may use the ‘Paint’ effect in the ‘Segment editor’ in a similar way, then use ‘Fill between slices’. You should get a well constructed segment, that can be further smoothed.

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**Author:** ![JiDafeng](https://avatars.discourse-cdn.com/v4/letter/j/ce73a5/32.png) [@JiDafeng](https://discourse.slicer.org/u/JiDafeng)\
**Post date:** [October 6, 2023, 2:38am UTC](https://discourse.slicer.org/t/vagina-segmentation-and-reconstruction-from-mri-image/31989/5 "2023-10-06T02:38:25Z")

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Could you save the lines as mesh which could be imported into 3dsMax.Then UV surface could be made according the lines.

 ![figure1](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/9/b9eba2186c5f7311ab3fee2d2c9beb975bc460b5.jpeg)  
 ![figure3](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/7/87faa8fadca19f771fda864b3f2e5222fd60305d.jpeg)  
 ![figure5](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/2/8/282f77702597462e252911013e04dbf66f7b8e84.jpeg)

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<div class="post-metadata">

**Author:** ![Miri\_Trope](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/miri_trope/32/67690_2.png) [@Miri\_Trope](https://discourse.slicer.org/u/Miri_Trope)\
**Post date:** [October 6, 2023, 2:00pm UTC](https://discourse.slicer.org/t/vagina-segmentation-and-reconstruction-from-mri-image/31989/6 "2023-10-06T14:00:52Z")

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Thank you for your response. Could you provide more information about how you incorporated the lines into a 3D surface? What software did you use for this task? Additionally, could you suggest any open-source software that you would recommend for performing this operation?