Creating Atlas of Brain MRI

Support
1

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.

2

That all sounds pretty doable - did you start by looking at the tutorials?

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.