# How to merge MRI and brain atlas

**URL:** <https://discourse.slicer.org/t/how-to-merge-mri-and-brain-atlas/5288>\
**Category:** Support\
**Tags:** lead-dbs\
**Created:** [January 6, 2019, 12:46pm UTC](https://discourse.slicer.org/t/how-to-merge-mri-and-brain-atlas/5288 "2019-01-06T12:46:07Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![flashman](https://avatars.discourse-cdn.com/v4/letter/f/3ec8ea/32.png) [@flashman](https://discourse.slicer.org/u/flashman)\
**Post date:** [January 6, 2019, 12:46pm UTC](https://discourse.slicer.org/t/how-to-merge-mri-and-brain-atlas/5288/1 "2019-01-06T12:46:07Z")

</div>

Operating system: Windows 10  
Slicer version: 4.10

Hi all,  
I am relatively new to the 3D Slicer program and currently undergoing the  
precise localization of electrodes after deep brain stimulation (DBS) surgery.  
I’ve constructed the shape of the electrodes. But the precise localization in the brian is still unknown. The targets the electrodes are bilateral subthalamic nucleus (STN).

How to merge the MRI images and the brain atlas to make the precise localization of electrodes?

Any advice for this? Thank for your help.

 ![SceneView](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/0/f0ac06f1c1ff2a789becf3f99ca7c870243faee1.png)

---

<div class="post-metadata">

**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:** [January 6, 2019, 4:38pm UTC](https://discourse.slicer.org/t/how-to-merge-mri-and-brain-atlas/5288/2 "2019-01-06T16:38:32Z")

</div>

This paper would be a good place to start:

[https://www.researchgate.net/publication/262075665\_PyDBS\_an\_automated\_image\_processing\_workflow\_for\_deep\_brain\_stimulation\_surgery](https://www.researchgate.net/publication/262075665_PyDBS_an_automated_image_processing_workflow_for_deep_brain_stimulation_surgery)

---

<div class="post-metadata">

**Author:** ![rkikinis](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rkikinis/32/791_2.png) [@rkikinis](https://discourse.slicer.org/u/rkikinis)\
**Post date:** [January 6, 2019, 5:07pm UTC](https://discourse.slicer.org/t/how-to-merge-mri-and-brain-atlas/5288/3 "2019-01-06T17:07:51Z")

</div>

STN might be easier to identify on the coronal views of your own data, if you used an isotropic resolution.

---

<div class="post-metadata">

**Author:** ![wpgao](https://avatars.discourse-cdn.com/v4/letter/w/8e8cbc/32.png) [@wpgao](https://discourse.slicer.org/u/wpgao)\
**Post date:** [January 7, 2019, 6:16am UTC](https://discourse.slicer.org/t/how-to-merge-mri-and-brain-atlas/5288/4 "2019-01-07T06:16:34Z")

</div>

Maybe you can refer to Lead-DBS, which has achieved such a goal! Some registration methods can be used to develop your own module for this!

---

<div class="post-metadata">

**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:** [June 18, 2022, 2:43pm UTC](https://discourse.slicer.org/t/how-to-merge-mri-and-brain-atlas/5288/6 "2022-06-18T14:43:31Z")

</div>

A post was split to a new topic: [Register LeadDBS atlas with patient image](https://discourse.slicer.org/t/register-leaddbs-atlas-with-patient-image/23926)