Human Brain Atlas Mesh Files


I was wondering if the Allen Institute provides structural meshes for a segmented human reference brain similar to the mouse ccf meshes provided here:

I know that these files exist:

But I can’t find any documentation on what these files are or how to use them to get meshes in a useable file type (.ply, .stl, .obj, etc.).

Thank you,


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Hi Jopeter,

Welcome to the forums!

I think you can use the linked files to generate stls. The trick is a 3rd-party application called itk-SNAP. Here are the steps that worked for me just now:

  1. install and open itk-SNAP
  2. Download the annotation file and load it as a main image into itk-SNAP by using File->Open Main Image. Now I see:
  3. Download the segmentation file. Load it into itk-SNAP via Segmentation->Open Segmentation. I now see:
  4. Click update in the bottom left to show meshes derived from this segmentation. This results in:
  5. To save meshes out, go to Segmentation->Export as Surface Mesh. This opens up a dialog, with options to export one or all meshes. I chose “separate files”, and on the next page of the dialog changed the file format to stl.

As a sanity check, I then imported these stls into blender. Looks alright!


Could not have been easier! Thank you immensely!

By the way, do you know if similar data files exist for the right hemisphere as well?