Open Atlas Followup


At the 2015 Winter Project Week, I presented and improved a project called Open Atlas. After that meeting, I did further improvements. Jesica Forbes and @hjmjohnson approached me about using the tools on their MRI BRAINS atlases. I made further improvements that made the tools useful for them. Jessica presented a poster called “Visualization and Utilization of Medical Imaging Atlas Correction Tools”. Susequently Jessica, Hans and others published “An Open-Source Label Atlas Correction Tool and Preliminary Results on Huntingtons Disease Whole-Brain MRI Atlases”.

I had put this project on the back burner. I recently rebuild it with newer vtk and itk versions.

Here are some of the features:

  1. Creates an adjacency map for each label.
  2. Creates statistics for each label.
  3. Generates STL files for each label.
  4. Generates.vtk files showing labeled voxels as cubes for each label.
  5. Generates screenshots with one viewport showing the .stl model and its adjacencies. The other viewport shows the .vtk cube models with its adjacencies. Views are selected automatically based on the left/right/centered label names.
  6. Generates a mrml scene for the atlas. The scene also has markups for labels that have disconnected regions.
  7. Generates “diff images” for edited labels.

Are these useful tools for the Slicer Community? If so, I’d be happy to work with someone to integrate some or all into Slicer.


BTW I’ve run the tools in the SPLBrainAtlas, SPLKneeAtlas, SPLHeadNeckAtlas, SPLAbdominalAtlas, ICBMBrainAtlas FreeSurferSampleAtlas and 107 Mindboggle segmentations.

1 Like

Hey Bill -

Thanks for keeping this going, looks great.

@jcfr and I will work on an extension for this code tomorrow.

Cheers from project week! (Actually from the post-hacking sushi bar outing).

1 Like

Hi Bill! Great to hear from you. Mike is sending you something.

Wish I was there to help. I sure miss Project Week.

Why not come again? How’re you doing?

And we are missing you


Doing well, but my traveling days are over…


How about joining by video conference? Just to say hello to everyone?