Visualization&art of whole brain tractography

Dear expertise of Mrtrix3,

Every time I visited the Mrtrix3 website, I cannot stop to enjoy those alluring images displayed on the home page, in particular for the 3D images of whole-brain tractography:

Best tractography arts:

I tried to make similar tractography arts using mrview for the species (marmosets) that I am working on.

However, the image of mine turned out to be miserable.

I understood that making a tractography arts is not a simple journey, and there will be many tricks about tracking, masking, lighting choice, etc.

Could you mind sharing your experience on how to make similar images that displayed on Mrtrix3 home page?

Do I need extra software to make the art image beside mrview?

Thanks and I would be highly appreciated if you could give me some hint.

Cirong Liu

Hi Cirong,

Probably the main thing you’re missing at the moment is track lighting. It’s off by default because it hurts performance, but as long as your number of streamlines is not absurd it runs quite well. Check near the bottom of the mrview Tractography tool.

Rob

Apart from lighting/shading, the trick to the top one is combining with an anatomical (or other) volume and playing with the opacity/transparency of that volume. That gives an extra sense of depth, because the “fog” of that volume gets denser the deeper you go into the view. Additionally, for that top one, note that I also used clip planes. You can’t easily see them, because the volume itself is so transparent, but it does make a significant difference in showing the front of that tractogram in bright colours, and only going “into the fog” closer to the back/side edge of the image.

You can find a few other examples animated and spinning live, on my YouTube channel: https://www.youtube.com/ThijsDhollander

There’s also a few other variants shown in this article, some of which might give you a few ideas on how to make these things look nice: https://www.abc.net.au/news/science/2019-08-12/brainbows-brain-image-tractography-neuroscience/11363764

Note that, apart from fancy-ness, a good sense of depth is also a very useful cue for visualisation and navigation. It’s more than just pretty pictures; making them pretty in specific ways can also be desirable for specific applications!

Hi,Rob and Dhollander,

Thanks a lot for the tips and tricks, which indeed very helpful.

Combining volume clip+transparent and tuning lighting (to create depth sense) improved the 3D image a lot, and played it is quite fun.

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No worries. It does take some practice, but at some point you learn the essential bits of the tools to produce good figures consistently. :slightly_smiling_face::+1: