Human Brain Atlas Mesh Files

Technical
, , , , , ,
1

Hello,

I was wondering if the Allen Institute provides structural meshes for a segmented human reference brain similar to the mouse ccf meshes provided here: http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/structure_meshes/ply/

I know that these files exist: http://download.alleninstitute.org/informatics-archive/allen_human_reference_atlas_3d_2020/version_1/examples/convert_to_itksnap/

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,

Jonah

1 Like
2

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:
    annot
    annot1704×1431 113 KB
  3. Download the segmentation file. Load it into itk-SNAP via Segmentation->Open Segmentation. I now see:
    segmentation
    segmentation1704×1431 119 KB
  4. Click update in the bottom left to show meshes derived from this segmentation. This results in:
    label_desc
    label_desc1704×1431 251 KB
  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!

looks_familiar
looks_familiar1265×893 818 KB

Cheers,
Nile

3

Could not have been easier! Thank you immensely!

4

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