# Division of the brain into individual parts

**URL:** <https://discourse.slicer.org/t/division-of-the-brain-into-individual-parts/47214>\
**Category:** Support\
**Created:** [June 2, 2026, 2:58pm UTC](https://discourse.slicer.org/t/division-of-the-brain-into-individual-parts/47214 "2026-06-02T14:58:27Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Tedy](https://avatars.discourse-cdn.com/v4/letter/t/bc79bd/32.png) [@Tedy](https://discourse.slicer.org/u/Tedy)\
**Post date:** [June 2, 2026, 2:58pm UTC](https://discourse.slicer.org/t/division-of-the-brain-into-individual-parts/47214/1 "2026-06-02T14:58:27Z")

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Hi, can someone please help me cut out the brain parts from an MRI?  
I had a brain tumor and I want to make 3D models of the parts of my brain that were compressed by the tumor. It will help me come to terms with the diagnosis, treatment, and it will help with education. Thank you very much

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**Author:** ![JASON](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jason/32/13419_2.png) [@JASON](https://discourse.slicer.org/u/JASON)\
**Post date:** [June 2, 2026, 7:18pm UTC](https://discourse.slicer.org/t/division-of-the-brain-into-individual-parts/47214/2 "2026-06-02T19:18:48Z")

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Hello Tedy,

Sorry to hear about the diagnosis, but welcome to the world of medical imaging!

There are a few AI brain segmentation models, but the easiest to use without installing anything is [https://brainchop.org/](https://brainchop.org/)

1. You can save your MRI image to NIFTI format (\*.nii.gz) and then drag & drop it into BrainChop.
2. There are a few different model options to choose from from model dropdown at the top.
3. Once it completes processing, press “Save Seg” button at the top to download the segmentation in NIFTI format.
4. Import the segmentation into 3D slicer (as ‘segmentation’ not as volume)
5. Press the 3D button to see it in the 3D view.

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<div class="post-metadata">

**Author:** ![JASON](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jason/32/13419_2.png) [@JASON](https://discourse.slicer.org/u/JASON)\
**Post date:** [June 2, 2026, 7:24pm UTC](https://discourse.slicer.org/t/division-of-the-brain-into-individual-parts/47214/3 "2026-06-02T19:24:37Z")

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These models are likely trained on healthy brains so may not capture tumor & compression accurately.

I’m working on a brain & tumor segmentation service, you’ll be able to sign up for a free trial when the patient-specific features are added in a few weeks:

> **[ATLAS Simulation](https://sim.atlasmeditech.com)**

If you would like to learn more about neurosurgery and patient resources, you may find these links useful:

> **[The Neurosurgical Atlas, by Aaron Cohen-Gadol, M.D.](https://www.neurosurgicalatlas.com/)**
>
> The most comprehensive and respected resource for advanced neurosurgical techniques in the world.

> **[Best Care for Your Brain Tumor](https://www.aaroncohen-gadol.com/en/patients/preface)**
>
> Get access to the best resource and necessary information on brain surgery for patients to make the best decision for care and promote life after surgery.