# Creating Atlas of Brain MRI

**URL:** <https://discourse.slicer.org/t/creating-atlas-of-brain-mri/3023>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [May 30, 2018, 6:43pm UTC](https://discourse.slicer.org/t/creating-atlas-of-brain-mri/3023 "2018-05-30T18:43:43Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![teresababy](https://avatars.discourse-cdn.com/v4/letter/t/5f9b8f/32.png) [@teresababy](https://discourse.slicer.org/u/teresababy)\
**Post date:** [May 30, 2018, 6:43pm UTC](https://discourse.slicer.org/t/creating-atlas-of-brain-mri/3023/1 "2018-05-30T18:43:44Z")

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Operating system: Windows 7  
Slicer version: 4.8.1

I am not sure how to begin this project. I have an MRI of my brain and I would like to segment and label all of the important anatomical structures, creating an atlas.

I have the files in Nifti format and plan to label a post GRE T1 scan acquired in the coronal plane.

First, I want to link this coronal scan with a scan acquired in the sagittal plane, as the some structures are more easily seen sagittaly.

Next, I want to segment out the important structures and label them with text indicating the name of the structures.

Finally, I would like to save the updated file as a Nifti.

I would probably be doing this all manually, as I am only slightly familiar with Python.\

How would I go about doing these things?

Thank You.

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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:** [May 31, 2018, 12:00am UTC](https://discourse.slicer.org/t/creating-atlas-of-brain-mri/3023/2 "2018-05-31T00:00:07Z")

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That all sounds pretty doable - did you start by looking at the [tutorials](https://www.slicer.org/wiki/Documentation/4.8/Training)?

Also, you probably know there are many brain atlases already available so you might want to do some background searching to see if you can use what’s already been done.