1. Neuroscience

Automated hippocampal unfolding for morphometry and subfield segmentation with HippUnfold

  1. Jordan DeKraker  Is a corresponding author
  2. Roy AM Haast
  3. Mohamed D Yousif
  4. Bradley Karat
  5. Jonathan C Lau
  6. Stefan Köhler
  7. Ali R Khan  Is a corresponding author
  1. University of Western Ontario, Canada
  2. Aix-Marseille University, France
https://doi.org/10.7554/eLife.77945
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  1. Jordan DeKraker
  2. Roy AM Haast
  3. Mohamed D Yousif
  4. Bradley Karat
  5. Jonathan C Lau
  6. Stefan Köhler
  7. Ali R Khan
(2022)
Automated hippocampal unfolding for morphometry and subfield segmentation with HippUnfold
eLife 11:e77945.
https://doi.org/10.7554/eLife.77945
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Abstract

Like neocortical structures, the archicortical hippocampus differs in its folding patterns across individuals. Here, we present an automated and robust BIDS-App, HippUnfold, for defining and indexing individual-specific hippocampal folding in MRI, analogous to popular tools used in neocortical reconstruction. Such tailoring is critical for inter-individual alignment, with topology serving as the basis for homology. This topological framework enables qualitatively new analyses of morphological and laminar structure in the hippocampus or its subfields. It is critical for refining current neuroimaging analyses at a meso- as well as micro-scale. HippUnfold uses state-of-the-art deep learning combined with previously developed topological constraints to generate uniquely folded surfaces to fit a given subject's hippocampal conformation. It is designed to work with commonly employed sub-millimetric MRI acquisitions, with possible extension to microscopic resolution. In this paper we describe the power of HippUnfold in feature extraction, and highlight its unique value compared to several extant hippocampal subfield analysis methods.

Data availability

All code for the HippUnfold application has been made available at https://github.com/khanlab/hippunfold. Data and code to generate the Figures shown in this study have been made available at https://zenodo.org/record/6360647.

The following previously published data sets were used

Article and author information

Author details

  1. Jordan DeKraker

    University of Western Ontario, London, Canada
    For correspondence
    jordan.dekraker@mail.mcgill.ca
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4093-0582

  2. Roy AM Haast

    Aix-Marseille University, Marseille, France
    Competing interests
    The authors declare that no competing interests exist.

  3. Mohamed D Yousif

    University of Western Ontario, London, Canada
    Competing interests
    The authors declare that no competing interests exist.

  4. Bradley Karat

    University of Western Ontario, London, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6550-1418

  5. Jonathan C Lau

    University of Western Ontario, London, Canada
    Competing interests
    The authors declare that no competing interests exist.

  6. Stefan Köhler

    Brain and Mind Institute, University of Western Ontario, london, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1905-6453

  7. Ali R Khan

    University of Western Ontario, London, Canada
    For correspondence
    alik@robarts.ca
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0760-8647

Funding

Canadian HIV Trials Network, Canadian Institutes of Health Research (366062)

  • Stefan Köhler
  • Ali R Khan

Canada Research Chairs (950-231964)

  • Ali R Khan

Natural Sciences and Engineering Research Council of Canada (6639)

  • Ali R Khan

Canada Foundation for Innovation (37427)

  • Ali R Khan

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Human subjects: Informed consent and consent to publish were obtained by the original authors of the open source data examined here. Each of the three datasets included research ethics board approvals, as well as informed consent and, in the HCP-Aging dataset, assessment of the subjects' ability to provide consent. For the single epilepsy patient case examined here, research ethics board approval and informed consent were collected at the Western University (HSREB # 108952, Lawson: R-17-156).

Reviewing Editor

  1. Birte U Forstmann, University of Amsterdam, Netherlands

Publication history

  1. Preprint posted: December 5, 2021 (view preprint)
  2. Received: February 17, 2022
  3. Accepted: December 13, 2022
  4. Accepted Manuscript published: December 15, 2022 (version 1)
  5. Version of Record published: January 10, 2023 (version 2)

Copyright

© 2022, DeKraker et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Jordan DeKraker
  2. Roy AM Haast
  3. Mohamed D Yousif
  4. Bradley Karat
  5. Jonathan C Lau
  6. Stefan Köhler
  7. Ali R Khan
(2022)
Automated hippocampal unfolding for morphometry and subfield segmentation with HippUnfold
eLife 11:e77945.
https://doi.org/10.7554/eLife.77945

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