goballooning / md-dmri-data

Example data to be processed with the md-dmri framework

Multidimensional diffusion MRI data

This repository contains some simple data sets suitable for getting acquainted with the MD-dMRI framework for processing multidimensional diffusion MRI data.¹ The data was acquired on a Bruker microimaging system with a custom diffusion-encoded RARE sequence² using gradient waveforms and q-trajectories³ giving axisymmetric b-tensors.⁴ The data was originally reported in

• Topgaard_NMRBiomed2019
• Jiang_MScProject2018
• Topgaard_PhysChemChemPhys2016.

How to start

• Download the MD-dMRI framework and add to the Matlab search path.
• Download this repository and locate a pdata_mddmri folder within for instance the Topgaard_NMRBiomed2019/SmallSpheres_BigSpheres_OrderedSticks data set.
• Run step1_recon.m to convert the raw Bruker data to nifti images and experimental parameters to matlab format.
• Run step2_fit.m to process the data with gamma,² covariance,⁵ and 4D diffusion tensor distribution.⁶
• View the images in the indata and fitdata/maps folders with the GUI started by typing mgui in the Matlab command window.
• Run step3_dtdbootstrap.m to perform uncertainty estimation for the 4D diffusion tensor distributions.⁶
• Run step4_dtdfigs.m to generate figures corresponding to Figs 3-7 in Topgaard_NMRBiomed2019.

References

1. D. Topgaard. Multidimensional diffusion MRI. J. Magn. Reson. 275, 98-113 (2017).
2. S. Lasič, F. Szczepankiewicz, S. Eriksson, M. Nilsson, D. Topgaard. Microanisotropy imaging: quantification of microscopic diffusion anisotropy and orientational order parameter by diffusion MRI with magic-angle spinning of the q-vector. Front. Physics 2, 11 (2014).
3. S. Eriksson, S. Lasič, D. Topgaard. Isotropic diffusion weighting by magic-angle spinning of the q-vector in PGSE NMR. J. Magn. Reson. 226, 13-18 (2013).
4. S. Eriksson, S. Lasič, M. Nilsson, C.-F. Westin, D. Topgaard. NMR diffusion encoding with axial symmetry and variable anisotropy: Distinguishing between prolate and oblate microscopic diffusion tensors with unknown orientation distribution. J. Chem. Phys. 142, 104201 (2015).
5. C.-F. Westin, H. Knutsson, O. Pasternak, F. Szczepankiewicz, E. Özarslan, D. van Westen, C. Mattisson, M. Bogren, L. O'Donnell, M. Kubicki, D. Topgaard, M. Nilsson. Q-space trajectory imaging for multidimensional diffusion MRI of the human brain. Neuroimage 135, 345-362 (2016).
6. D. Topgaard. Diffusion tensor distribution imaging. NMR Biomed., e4066 (2019).