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Joint modelling of diffusion MRI and microscopy

Howard, Amy F.D.; Mollink, Jeroen; Kleinnijenhuis, Michiel; Pallebage-Gamarallage, Menuka; Bastiani, Matteo; Cottaar, Michiel; Miller, Karla L.; Jbabdi, Saad


Amy F.D. Howard

Jeroen Mollink

Michiel Kleinnijenhuis

Menuka Pallebage-Gamarallage

Matteo Bastiani

Michiel Cottaar

Karla L. Miller

Saad Jbabdi


The combination of diffusion MRI (dMRI) with microscopy provides unique opportunities to study microstructural features of tissue, particularly when acquired in the same sample. Microscopy is frequently used to validate dMRI microstructure models, addressing the indirect nature of dMRI signals. Typically, these modalities are analysed separately, and microscopy is taken as a gold standard against which dMRI-derived parameters are validated. Here we propose an alternative approach in which we combine dMRI and microscopy data obtained from the same tissue sample to drive a single, joint model. This simultaneous analysis allows us to take advantage of the breadth of information provided by complementary data acquired from different modalities. By applying this framework to a spherical-deconvolution analysis, we are able to overcome a known degeneracy between fibre dispersion and radial diffusion. Spherical-deconvolution based approaches typically estimate a global fibre response function to determine the fibre orientation distribution in each voxel. However, the assumption of a ‘brain-wide’ fibre response function may be challenged if the diffusion characteristics of white matter vary across the brain. Using a generative joint dMRI-histology model, we demonstrate that the fibre response function is dependent on local anatomy, and that current spherical-deconvolution based models may be overestimating dispersion and underestimating the number of distinct fibre populations per voxel.


Howard, A. F., Mollink, J., Kleinnijenhuis, M., Pallebage-Gamarallage, M., Bastiani, M., Cottaar, M., …Jbabdi, S. (2019). Joint modelling of diffusion MRI and microscopy. NeuroImage, 201,

Journal Article Type Article
Acceptance Date Jul 11, 2019
Online Publication Date Jul 14, 2019
Publication Date Nov 1, 2019
Deposit Date Jul 31, 2019
Publicly Available Date Aug 23, 2019
Journal NeuroImage
Print ISSN 1053-8119
Electronic ISSN 1095-9572
Publisher Elsevier
Peer Reviewed Peer Reviewed
Volume 201
Article Number 116014
Keywords Diffusion MRI; Histology; White matter; Fibre response function; Orientation dispersion
Public URL
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