ArticlebioRxiv : the preprint server for biology2026
DEEP-LEARNING CORTICAL REGISTRATION GUIDED BY STRUCTURAL AND DIFFUSION MRI AND CONNECTIVITY.
Zhen Zhou, Jian Li, Jonathan Williams, Bruce Fischl, Iman Aganj
Abstract readPreprint
In one paragraphArticle in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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0citing papers in PubMed
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What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
2 · The registryThe trial behind it
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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
3 · Its place in the literatureWho cites it
0 citing papers in PubMed.
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4 · The recordCorrections and comments
5 · Who and what moneyAuthors and funding
5 authors.
Zhen ZhouAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.ORCID 0000-0002-9169-5885 Jian LiAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.ORCID 0000-0002-1691-8727 Jonathan WilliamsAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.
Bruce FischlAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.
Iman AganjAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.ORCID 0000-0002-4673-1293 Funding
Functionally guided adult whole brain cell atlas in human and NHPUM1MH130981 · NIMH · ALLEN INSTITUTE · PI Ed Lein, Hongkui Zeng · 2022 to 2026
$91.9MCenter for Multi-Scale Multi-Omic Human and non-human primate Brain AtlasUM1MH134812 · NIMH · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Kwanghun Chung, PATRICK R HOF · 2025 to 2026
$21.7MBRAIN CONNECTS: The center for Large-scale Imaging of Neural Circuits (LINC)UM1NS132358 · NINDS · MASSACHUSETTS GENERAL HOSPITAL · PI Suzanne N Haber, Elizabeth M. C. Hillman · 2023 to 2026
$17.5MMRI, Genetics &Cognitive Precursors of AD &DementiaR01AG016495 · NIA · BOSTON UNIVERSITY MEDICAL CAMPUS · PI AU, RHODA · 1999 to 2016
$12.5MThe Human Connectome Project (HCP)U01MH093765 · NIMH · MASSACHUSETTS GENERAL HOSPITAL · PI ROSEN, BRUCE R · 2010 to 2014
$12.1MTraining and Dissemination CoreP41EB030006 · NIBIB · MASSACHUSETTS GENERAL HOSPITAL · PI Susie Yi Huang, BRUCE R ROSEN · 2020 to 2026
$10.9MLate-onset Unexplained Epilepsy as a Risk Factor for DementiaR01NS130119 · NINDS · MASSACHUSETTS GENERAL HOSPITAL · PI Alice D Lam · 2023 to 2026
$8.7MImaging and Analysis Techniques to Construct a Cell Census Atlas of the Human Brain Admin SupplementU01MH117023 · NIMH · MASSACHUSETTS GENERAL HOSPITAL · PI BOAS, DAVID A, FISCHL, BRUCE · 2018 to 2022
$7.6MAn Acquisition and Analysis Pipeline for Integrating MRI and Neuropathology in TBI-related Dementia and VCIDU24NS135561 · NINDS · MASSACHUSETTS GENERAL HOSPITAL · PI Bruce Fischl, Susie Yi Huang · 2023 to 2026
$6.1MFreeSurfer Development, Maintenance, and HardeningR01EB023281 · NIBIB · MASSACHUSETTS GENERAL HOSPITAL · PI Bruce Fischl, Douglas Nowlin Greve · 2016 to 2026
$5.6MClinical & biological signatures of post-traumatic neurodegeneration: Leveraging the TBI Model Systems of Care to accelerate in vivo diagnosis of the late effects of TBI (LETBI)RF1NS128961 · NINDS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI DAMS-O'CONNOR, KRISTEN · 2022 to 2022
$5.0MA Longitudinal Analysis Stream for FreeSurferR01NS083534 · NINDS · MASSACHUSETTS GENERAL HOSPITAL · PI Bruce Fischl · 2014 to 2026
$4.6MNCRR NIH HHS S10 RR019307NCRR NIH HHS S10 RR023043NCRR NIH HHS S10 RR023401NIA NIH HHS R01 AG016495NIA NIH HHS R01 AG064027NIA NIH HHS R01 AG068261NIA NIH HHS R01 AG070988NIA NIH HHS R21 AG082082NIBIB NIH HHS P41 EB030006NIBIB NIH HHS R01 EB019956NIBIB NIH HHS R01 EB023281NIBIB NIH HHS R21 EB018907NIMH NIH HHS RF1 MH121885NIMH NIH HHS RF1 MH123195NIMH NIH HHS U01 MH093765NIMH NIH HHS U01 MH117023NIMH NIH HHS UM1 MH130981NIMH NIH HHS UM1 MH134812NINDS NIH HHS R01 NS070963NINDS NIH HHS R01 NS083534NINDS NIH HHS R01 NS105820NINDS NIH HHS R01 NS130119NINDS NIH HHS R25 NS125599NINDS NIH HHS RF1 NS128961NINDS NIH HHS U01 NS132181NINDS NIH HHS U24 NS135561NINDS NIH HHS UM1 NS132358
6 · The paper itselfAbstract
Accurate cortical surface registration is crucial for group-level neuroimaging analyses, yet geometry-based methods often yield suboptimal functional alignment across subjects due to substantial inter-individual variability. We present a novel deep-learning approach that incorporates white matter structural connectivity features from diffusion MRI (dMRI) tractography into the Joint Surface-based Registration and Atlas Construction (JOSA) framework. Our method generates vertex-wise connectivity maps by detecting streamline-surface intersections, followed by heat diffusion smoothing on the cortical manifold. We combine these connectivity features with scalar diffusion metrics (fractional anisotropy and apparent diffusion coefficient) and structural features as input to JOSA (which we call "JOSAConn"). Evaluated on HCP-YA subjects across 15 task contrasts, our method significantly outperforms FreeSurfer in functional alignment (Bonferroni-corrected
Indexed as
Cortical surface registrationfunctional alignmentheat diffusion smoothingsemi-supervised learning
Identifiers
PMID41278765
PMCPMC12637582
What OpenQuestion holds
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