User:Was a bee/Tractography

How to import human brain white matter tracts to Blender.

HCP Tractography Atlas

Cingulum from the HCP Tractography Atlas. (The polygon data of the skull and the brain are from BodyParts3d.)

The HCP Tractography Atlas (Fang-Cheng Yeh et al., 2018 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6921501/ ) is available under the CC-BY-SA-4.0 license.

• 1. Go to HCP Tractography Atlas page. http://brain.labsolver.org/diffusion-mri-templates/tractography
• 2. Download the tract files, TT format or TRK format. I chose TRK format. But I think both work.
• 3. Download the HCP-1065 template fib file.
• 4. Download and Install the DSI studio (free software) at http://dsi-studio.labsolver.org/dsi-studio-download
• 5. Run the DSI Studio and click the [Step T3 Fiber Tracking] and choose the HCP-1065 template fib file.
• 6. Then the *.tt.gz or trk.gz files can be loaded using [Tracts][Open Tracts].
• 7. Select the tract you want at the list at the right. Then save the tract as .wrl file format using [Tracts][Save Tracts][Save VRML].
• 8. In Blender, use [File][Import][X3D Extensible 3D (.x3d/.wrl)]. Then the tract appears as polygon in Blender.

ISMRM 2015 Tractography Challenge data

The ISMRM 2015 Tractography Challenge data (Klaus H. Maier-Hein et al., 2018 https://dx.doi.org/10.1038%2Fs41467-017-01285-x ) is available under the CC-BY-4.0 license.

• 1. Go to the data distribution page. https://zenodo.org/record/572345

Data size

Data size of tract files are generally very huge.

For example, data size of the polygon of the cingulum (image at the top-right) is about 700MB in wrl file format.

So, if your PC doesn't have huge RAM, Blender can't treat tract data smoothly. (Blender works but it is very slow. Because of frequent memory swapping between RAM and HDD.)

As of 2021, I currently use PC which has 32GB RAM (and 8GB video RAM). 32GB RAM size is insane for normal purpose (e.g. reading Wikipedia, watching YouTube, playing online games, and so on). Today, this size is generally used only by Video/CGI editing people.

Here what I want to say is "My PC is cool!" "If you bought your PC in normal way and you haven't upgraded, your PC very likely doesn't have enough RAM for treating tract data in Blender."

As of 2021, it is possible to buy 32GB RAM about $200 at Amazon.com or somewhere else. So if your PC can't handle tract data smoothly, try to consider upgrading RAM for your PC.