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Updated: Sep 3, 2026

Co-analysis of Brain Structure and Function using fMRI and Diffusion-weighted Imaging
Published on: November 8, 2012
Bridging the microstructural gap in human connectomics using hierarchical phase-contrast tomography as a reference
Eric Wanjau1,2, Matthieu Chourrout2,3, Chiara Maffei3
1Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
Abstract:
Diffusion MRI (dMRI) allows us to image the human connectome non-invasively, yet it provides indirect estimates of axonal orientations based on the diffusion of water molecules in millimeter-scale voxels, hence struggling to resolve complex micrometer-scale fiber geometries. Invasive methods for imaging axonal orientations ex vivo, e.g. histology, are destructive and limited to small volumes, creating a critical need for a non-destructive modality for imaging microscopic fiber orientations in 3D. Here, we use Hierarchical Phase-Contrast Tomography (HiP-CT) to characterize white matter architecture at the microscale. Applying structuretensor analysis to HiP-CT data, we compute fiber Orientation Distribution Functions and perform tractography analogous to dMRI. Across multiple brain regions, HiP-CT derived fiber architecture shows strong correspondence with that derived from dMRI while revealing substantially greater microstructural complexity. Despite its label-free nature, we demonstrate that vascular structures minimally confound HiP-CT orientation estimates. These results establish HiP-CT as a reference microscopic modality that can complement dMRI in multi-scale studies of white-matter organization.
Insights
Hierarchical Phase-Contrast Tomography (HiP-CT) non-destructively images brain white matter at the microscale. This method reveals greater microstructural complexity than diffusion MRI (dMRI), offering a new tool for connectome research.
Area of Science:
- Neuroimaging
- Biophysics
- Materials Science
Background:
- Diffusion MRI (dMRI) non-invasively images the human connectome but struggles with micrometer-scale axonal geometries due to water diffusion limitations.
- Invasive histology methods are destructive and limited to small volumes, highlighting a need for non-destructive 3D microscopic imaging of white matter fiber orientations.
Purpose of the Study:
- To utilize Hierarchical Phase-Contrast Tomography (HiP-CT) for characterizing white matter architecture at the microscale.
- To compare HiP-CT derived fiber architecture with dMRI data and assess its potential as a reference modality.
Main Methods:
- Applied structure-tensor analysis to HiP-CT data to compute fiber Orientation Distribution Functions.
- Performed tractography analogous to dMRI using HiP-CT derived orientation data.
- Evaluated the impact of vascular structures on HiP-CT orientation estimates.
Main Results:
- HiP-CT data revealed substantially greater microstructural complexity in white matter fiber architecture compared to dMRI.
- Strong correspondence was observed between fiber architecture derived from HiP-CT and dMRI across multiple brain regions.
- Vascular structures were found to minimally confound HiP-CT orientation estimates despite its label-free nature.
Conclusions:
- HiP-CT is established as a valuable non-destructive reference modality for imaging microscopic white matter architecture.
- HiP-CT complements dMRI by providing higher-resolution insights into microstructural complexity.
- This technique facilitates multi-scale studies of white matter organization and the human connectome.
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