# Team needed to develop a Magnetic Ressonance segmentation of the spinal column

**URL:** <https://discourse.slicer.org/t/team-needed-to-develop-a-magnetic-ressonance-segmentation-of-the-spinal-column/20189>\
**Category:** Support\
**Tags:** segmentation, mri, spine\
**Created:** [October 16, 2021, 11:43pm UTC](https://discourse.slicer.org/t/team-needed-to-develop-a-magnetic-ressonance-segmentation-of-the-spinal-column/20189 "2021-10-16T23:43:03Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Ricardoneuro](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ricardoneuro/32/4240_2.png) [@Ricardoneuro](https://discourse.slicer.org/u/Ricardoneuro)\
**Post date:** [October 16, 2021, 11:43pm UTC](https://discourse.slicer.org/t/team-needed-to-develop-a-magnetic-ressonance-segmentation-of-the-spinal-column/20189/1 "2021-10-16T23:43:03Z")

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I have been using a very efficient column volumetric magnetic resonance protocol for the past 5 years. I’m looking for a group of people interested in a segmentation protocol that can extract and segment bone tissue from a volumetric MRI file. I can see a very important use for this technology, specifically in the infant population, in order to generate volumetric reconstructions of the spine without exposure to ionizing radiation.

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**Author:** ![robertsoakes](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/robertsoakes/32/11042_2.png) [@robertsoakes](https://discourse.slicer.org/u/robertsoakes)\
**Post date:** [October 17, 2021, 5:24pm UTC](https://discourse.slicer.org/t/team-needed-to-develop-a-magnetic-ressonance-segmentation-of-the-spinal-column/20189/2 "2021-10-17T17:24:58Z")

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Hi Ricardo, this sounds like a fascinating project. MRI is a wonderful modality that is underutilized for procedure planning (at least in my opinion). Can you elaborate on the technical aims of what you are trying to accomplish?

It sounds like you’ve already accumulated a pretty good dataset, do you also have masks or models for some of them? Would a reference set need to be generated and validated as a starting point?

What degree of automation is needed? Is the goal to have a model that can create accurate masks without supervision or would operators be able to refine the masks before they are used downstream?

Is the goal purely research, or do you have specific applications (procedure planning, surgical navigation, 3D printing) which should be taken into account as part of the protocol design?

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**Author:** ![S\_Arbabi](https://avatars.discourse-cdn.com/v4/letter/s/dfb087/32.png) [@S\_Arbabi](https://discourse.slicer.org/u/S_Arbabi)\
**Post date:** [October 17, 2021, 7:14pm UTC](https://discourse.slicer.org/t/team-needed-to-develop-a-magnetic-ressonance-segmentation-of-the-spinal-column/20189/3 "2021-10-17T19:14:19Z")

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Dear @Ricardoneuro,

Great idea. I know of a company doing this task as a commercial software. That might be interesting for your question.  
My PhD supervisor (Dr. Peter Seevinck) started working on the idea of generating synthetic CT images from MR images 5 years ago and the deep learning-based softwate product recently has extended CE marks for spine as well.  
Here’s one study evaluating usage of this sCT spine for surgical planning:

> **[Magnetic resonance imaging–based synthetic computed tomography of the lumbar...](https://thejns.org/focus/view/journals/neurosurg-focus/50/1/article-pE13.xml)**
>
> OBJECTIVE Computed tomography scanning of the lumbar spine incurs a radiation dose ranging from 3.5 mSv to 19.5 mSv as well as relevant costs and is commonly necessary for spinal neuronavigation. Mitigation of the need for treatment-planning CT scans...

The company is MRIGuidance:

> **[BoneMRI now available for lower back - MRIguidance](https://mriguidance.com/bonemri-now-available-for-lower-back/)**
>
> For the first time the involvement of both the vertebra and the soft tissue of the spine, in patients with chronic back pain, can be examined from a single medical imaging exam. MRIguidance has extended its CE certificate of BoneMRI for usage in the...

Best,  
Saeed

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**Author:** ![diazandr3s](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/diazandr3s/32/9973_2.png) [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)\
**Post date:** [October 17, 2021, 8:48pm UTC](https://discourse.slicer.org/t/team-needed-to-develop-a-magnetic-ressonance-segmentation-of-the-spinal-column/20189/4 "2021-10-17T20:48:08Z")

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This is an interesting task. Have you considered utilising MONAI Label with the DeepEdit App ([MONAILabel/sample-apps/deepedit at main · Project-MONAI/MONAILabel · GitHub](https://github.com/Project-MONAI/MONAILabel/tree/main/sample-apps/deepedit))?

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**Author:** ![Lucas\_Formighieri](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lucas_formighieri/32/3266_2.png) [@Lucas\_Formighieri](https://discourse.slicer.org/u/Lucas_Formighieri)\
**Post date:** [October 31, 2021, 8:13pm UTC](https://discourse.slicer.org/t/team-needed-to-develop-a-magnetic-ressonance-segmentation-of-the-spinal-column/20189/5 "2021-10-31T20:13:49Z")

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Hi. I´ve been doing segmentation and 3D printing of medical exams for some time. I would surely like to help in anyway I can.  
Best regards,  
Lucas