Ex vivo diffusion MRI data from traumatic brain injury and sham operated rats

Abstract

This ex vivo diffusion MRI data corresponds to the extracted brains of five adult male Sprague-Dawley rats (10 weeks old, weights between 320 and 380 g). TBI was induced by lateral fluid percussion injury in three rats [1-3], while the other two rats went through a sham operation.

The MRI acquisitions were performed at room temperature (21 degrees Celsius) in a vertical 9.4 T/89 mm magnet. The dMRI data was acquired using a 3d segmented spin-echo EPI sequence with four segments and 0.150 mm x 0.150 mm x 0.150 mm resolution (data matrix 128 x 96 x 96, FOV 19.2 mm x 14.4 mm x 14.4 mm). TE/TR =35/1000 ms. The acquisition comprised a total of 132 volumes that consisted of 3 sets of 43 uniformly distributed directions with diffusion weighting (b-values) of 2, 3, and 4 ms/mm2, pulse length of 6 ms, and inter-pulse duration of 11.5 ms. Three non-diffusion-weighted images were also collected.

In order to improve the quality of the images for further analysis, the diffusion MRI data was processed following the steps in the DESIGNER pipeline [1,4] adapted for ex vivo diffusion MRI rat brains.

Besides the raw and processed diffusion MRI volumes, their b-values and b-vectors, we also provide brain masks, noise maps, and manually delineated white matter regions of interest of the corpus callosum, cingulum, and their crossing region in the ipsi- and contralateral side, which can be useful for further analysis.

Please, find the "README" file for further information regarding the data. You can also find details in the "Methods" sections of references [1-3].

Please cite the datasets as follows: Coronado-Leija, R., Abdollahzadeh, A., Lee, H.H., Coelho, S., Ades-Aron, B., Liao, Y., Salo, R.A., Tohka, J., Sierra, A., Novikov, D.S., and Fieremans, E. Ex vivo diffusion MRI data from traumatic brain injury and sham-operated rats (2024).

References:

[1] Ricardo Coronado-Leija, Ali Abdollahzadeh, Hong-Hsi Lee, Santiago Coelho, Benjamin Ades-Aron, Ying Liao, Raimo A. Salo, Jussi Tohka, Alejandra Sierra, Dmitry S. Novikov, and Els Fieremans. Volume electron microscopy in injured rat brain validates white matter microstructure metrics from diffusion MRI. arXiv preprint (2023).

[2] Raimo A Salo, Ilya Belevich, Eppu Manninen, Eija Jokitalo, Olli Grohn, Alejandra Sierra. Quantification of anisotropy and orientation in 3D electron microscopy and diffusion tensor imaging in injured rat brain. Neuroimage 172:404-414 (2018).

[3] Raimo A Salo, Ilya Belevich, Eija Jokitalo, Olli Grohn, Alejandra Sierra. Assessment of the structural complexity of diffusion MRI voxels using 3D electron microscopy in the rat brain and orientation in 3D electron microscopy and diffusion tensor imaging in injured rat brain. Neuroimage 225:117529 (2021).

[4] B. Ades-Aron, J. Veraart, P. Kochunov, S. McGuire, P. Sherman, E. Kellner, D. S. Novikov, and E. Fieremans, Evaluation of the accuracy and precision of the diffusion parameter estimation with Gibbs and noise removal pipeline, Neuroimage 183, 532 (2018).