Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Research Briefing
  • Published:

Krakencoder unifies diverse estimates of brain connectivity

In neuroscience, numerous complementary techniques have been established to estimate human brain connections in vivo. We have created a tool that aligns complementary views of brain connectivity into a unified latent representation. This tool can then translate among patterns of white matter connectivity and functional coactivation, across myriad estimation techniques, preserving inter-individual variability.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Krakencoder autoencoder architecture with shared latent representation.

References

  1. Gu, Z. et al. Heritability and interindividual variability of regional structure-function coupling. Nat. Commun. 12, 4894 (2021). This paper reports that regional differences in the structure–function relationship vary with age, sex and cognition.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Pervaiz, U. et al. Optimising network modelling methods for fMRI. Neuroimage 211, 116604 (2020). This paper systematically compares many common strategies for estimating functional connectivity, demonstrating the impact on reproducibility and phenotypic prediction.

    Article  PubMed  Google Scholar 

  3. Sarwar, T. et al. Mapping connectomes with diffusion MRI: deterministic or probabilistic tractography? Magn. Reson. Med. 81, 1368–1384 (2019). This paper used realistic simulations to demonstrate the possibility of false-positive connections with probabilistic tractography.

    Article  PubMed  Google Scholar 

  4. Messé, A. Parcellation influence on the connectivity-based structure–function relationship in the human brain. Hum. Brain Mapp. 41, 1167–1180 (2020). This paper demonstrates that the structure–function relationship can appear to change when using different brain segmentation approaches.

    Article  PubMed  Google Scholar 

  5. Zalesky, A. et al. Predicting an individual’s functional connectivity from their structural connectome: Evaluation of evidence, recommendations, and future prospects. Netw. Neurosci. 8, 1291–1309 (2024). A review article that explores connectome prediction performance and recommends future work include individual identifiability when assessing predictions.

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This is a summary of: Jamison, K. W. et al. Krakencoder: a unified brain connectome translation and fusion tool. Nat. Methods https://doi.org/10.1038/s41592-025-02706-2 (2025).

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Krakencoder unifies diverse estimates of brain connectivity. Nat Methods 22, 1406–1407 (2025). https://doi.org/10.1038/s41592-025-02705-3

Download citation

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41592-025-02705-3

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing