3D-MI-Reports

Visualization of complex Medical Imaging data such as functional connectivity, tractography, functional imaging and Multiparametric Tissue Signatures is a challenge. Recombining such data produces an even more complex problem concerning to medical interpretations.

Many different visualization solutions have been proposed. Margulies et al (2013) [1] and Rojas et al (2011; 2013) [2-3], for example, describe 2D as well as 3D neuroimaging visualization methods for tractography and functional connectivity data.

Aplications

3D Medical Imaging Report

We introduce a new concept of visualization in Medical Imaging biomarkers field through web and smartphones with this prototype.

10k

A graphical visualization for rapid view of brain statistics using three different programs: FreeSurfer, VolBrain and CERES

10K FreeSurfer

10k VolBrain

10k CERES

References

[1] Margulies, D.S., Böttger, J., Watanabe A., Gorgolewski, K.J., (2013).'Visualizing the human connectome' ,NeuroImage 80 (2013): 445-461.

[2] Rojas, G.M., Gálvez, M., Cordovez, J., Margulies, D.S., Castellanos, F.X., Milham, M.P., (2011). 'Applications of Stereoscopic 3D in Morphometric and Functional Imaging', HBM 2011, Quebec City, Canada.

[3] Rojas, G.M., Gálvez, M. (2013). 'Functional Connectivity Networks obtained using 10-20 EEG and 7 standard functional networks', HBM 2013, Seattle, USA.

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GitHub Pages Deployment

This repository is configured for automatic static deployment using GitHub Pages.

Structure

Root level index.html provides a simple navigation landing page linking to:

• brain-visualization/index.html
• spine-visualization/index.html
• brain-statistics/free-surfer/index.html (and related variant pages index_volbrain.html, index_ceres.html)

All asset/script references are relative; no leading slashes are used, so they work under the Pages subpath.

Workflow

The GitHub Actions workflow .github/workflows/deploy-pages.yml publishes the entire repository contents to Pages on every push to the master branch.

First-time Activation

1. Go to: Repository Settings → Pages.
2. Set Source = GitHub Actions (should auto-detect after first successful run).
3. After the workflow finishes, the site will be available at: https://<org-or-user>.github.io/3D-MI-Reports/

Direct links (assuming the BIMCV-CSUSP organization):

• Root portal: https://bimcv-csusp.github.io/3D-MI-Reports/
• Brain viewer: https://bimcv-csusp.github.io/3D-MI-Reports/brain-visualization/
• Spine viewer: https://bimcv-csusp.github.io/3D-MI-Reports/spine-visualization/
• FreeSurfer stats: https://bimcv-csusp.github.io/3D-MI-Reports/brain-statistics/free-surfer/

Local Preview

Serve locally with any static server from the repository root, e.g.:

python3 -m http.server 8000
# Then open http://localhost:8000/

Adding New Demos

1. Create a new folder at repository root (e.g., new-demo/).
2. Add its own index.html and assets with relative paths.
3. Link it from the root index.html grid.
4. Commit & push; the workflow redeploys automatically.

Troubleshooting

• If assets 404 on Pages but not locally: ensure paths are relative (./webgl/lib/three.js or webgl/lib/three.js, not /webgl/...).
• Clear browser cache or use a hard reload (Ctrl+Shift+R) after redeployments.
• Check Actions tab for any workflow failures.