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!