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Diffusion Weighted MR Imaging of Post-Mortem Rat Brain to Allow Reconstruction of the Cortical Connectome

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This dataset provides diffusion-weighted MRI (dMRI) and high-resolution 3D structural MRI of post-mortem rat brains, enabling detailed reconstruction of the cortical connectome.
It accompanies the publication by Sinke et al. (2018) and includes 10 perfusion-fixed Wistar rat brains scanned at ultra-high field (9.4 T).
The dataset contains raw dMRI and balanced SSFP data, along with derived diffusion metrics and anatomical references for connectome analysis.

All experiments were approved by the Animal Experiments Committee of the University Medical Center Utrecht and Utrecht University, and conducted in compliance with the European Communities Council Directive on animal research.

License

Creative Commons Attribution 4.0 International (CC BY 4.0)

Citation

Sinke, M. R. T., Otte, W. M., van der Toorn, A., Dijkhuizen, R., & Sarabdjitsingh, R. A. (2024).
Diffusion weighted MR imaging of post-mortem rat brain to allow reconstruction of the cortical connectome [Data set].
Brain Structure and Function, 223(5). Zenodo.
https://doi.org/10.5281/zenodo.11119038

Source

https://doi.org/10.5281/zenodo.11119038
Contact: m.r.t.sinke@umcutrecht.nl
Institution: University Medical Center Utrecht
Journal: Brain Structure and Function, 223(5), 2024

Dataset Information

Category Details
Species Rat (Rattus norvegicus, Wistar, male, 12–13 weeks old)
Sample Size 10 post-mortem brains
Preparation Perfusion-fixed via transcardial fixation; skulls intact
Scanner Varian 9.4 T horizontal bore system
Coil Custom solenoid coil (2.6 cm ID)
Imaging Medium Non-magnetic oil (Fomblin, Solvay Solexis)
Ethics Approval University Medical Center Utrecht (EU Directive compliant)
Institutions UMC Utrecht, Utrecht University

Purpose

The dataset supports investigation of rat cortical microstructure and connectivity using ex-vivo diffusion MRI.
It enables validation of diffusion tractography and modeling of cortical connectivity at high resolution, providing a reference for algorithm development, structural mapping, and interspecies comparison.

MR Acquisition Details

  • Diffusion MRI

    • 3D diffusion-weighted spin-echo sequence
    • Isotropic resolution: 150 μm
    • TR/TE: 500/32.4 ms
    • 60 diffusion-weighted directions (b = 1031–7756 s/mm²)
    • 24 b₀ images
    • Total: 325 images

  • Balanced SSFP (BSSFP)

    • 4 × 3D acquisitions, isotropic 100 μm
    • TR/TE: 15.4/7.7 ms, flip angle 40°
    • Phase shifts: 0°, 90°, 180°, 270°
    • Combined to reduce banding artifacts

  • Spoiled Gradient Echo (SPGR)

    • Echo times: 5, 10, 15 ms
    • TR: 20 ms, flip angle 40°
    • 24 averages

File Information

File Description Size Checksum
rawdata.zip NIfTI volumes for all 10 rats (RCR01–RCR10) including diffusion, BSSFP, and SPGR data 12.9 GB md5:f39aa478e8a8d9990843257d2c451ef6
derivatives.zip DTIfit-derived diffusion maps (FA, MD, etc.) and masks 621.9 MB md5:e45d3395f7affc3788a7824c31eedbe8
RCR_table.csv Acquisition metadata per animal 830 B md5:d0428a879d003d1243789f03b9820059
Sinke_BrainStructureFunction2018.pdf Associated publication 4.0 MB md5:938dac3d4452e5006f6628c3586ec41a
READ_ME.txt Original dataset description 4.9 kB md5:49e5fc005bc47bc6b2ca6bc864ba66bc

Keywords

MRI • Diffusion MRI • Rat Brain • Post-mortem • Cortical Connectome • High-field MRI • Ex-vivo Imaging • Tractography

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