DOI: 10.5281/zenodo.11119037
title: Diffusion weighted MR imaging of post-mortem rat brain to allow reconstruction of the cortical connectome

description: Brief description

 

These data accompany the article by Sinke et al. (Sinke et al., 2018). It contains the dMRI image volumes of 10 rats, a subset of these data was used for the tractography procedures described in the article. In addition high-resolution 3D balanced SSFP data are provided with high contrast between grey and white matter and CBF. The data are also accompanied by T1 weighted 3D spoiled gradient echo volumes at three different echo times (5,10 and 15 ms) which can be used for T2* measurements.

Animals

 

All animal procedures were approved by the Animal Experiments Committee of the University Medical Center Utrecht and Utrecht University. Experiments were performed in accordance with the guidelines of the European Communities Council Directive. Ten healthy adult (12–13 weeks old) male Wistar rats have been used and are described in the RCR_table.csv file. Animals were sacrificed and their brains were fixed with transcardial perfusion-fixation. Brains were extracted scanned.

 

MR acquisition

 

MRI was performed on a 9.4 T horizontal bore MR system (Varian, Palo Alto, CA, USA) equipped with a 6 cm ID gradient insert with gradients up to 1 T/m. A custom made solenoid coil with an internal diameter of 2.6 cm was used for excitation and reception of the MR signal. The perfusion-fixed brains were inserted with the skulls intact in a custom-made holder and immersed in non-magnetic oil (Fomblin, Solvay Solexis). Diffusion MR used a 3D diffusion-weighted spin-echo sequence with an isotropic spatial resolution of 150 mm, where the read- and phase- encode direction were  acquired using 8-shot EPI encoding and the second phase direction was linearly phase-encoded (TR/TE 500/32.4 ms, 220*128*108 matrix, FOV 33*19.2*16 mm3, D/d 15/4 ms, b 1031,2078,3994,6038,7756 s/mm2, 60 diffusion-weighted images in non-collinear directions and 24 images without diffusion weighting (b=0), number of averages 1, total number of images 325). Four 3D BSSFP images were acquired with an isotropic spatial resolution of 100 mm (TR/TE 15.4/7.7 ms, flip angle 40°, 320*160*190 matrix, FOV 32*16*19 mm3, 6 averages, pulse angle shift 0°, 90°, 180° and 270°). The four images were added as complex images to obtain a single BSSFP image with reduced banding artifacts in the brain. If scanning time allowed, three spoiled gradient-echo acquisitions were also performed with varying echotimes of 15, 10 and 5 ms respectively and TR 20 ms  (flip angle 40°, 320*160*190 matrix, FOV 32*16*19 mm3, 24 averages, pulse angle shift 117°).

Data structure

 

The repository contains the following data:

-       READ_ME.txt: this file

-       RCR_table.csv : Table containing acquisition dates and numbers for the scanned animals.

-       rawdata.zip : Zipped data directory ‘rawdata’ containing acquired images in NIfTI data format per animal. Data can be unzipped using the ‘unzip’ command. Directory rawdata contains subdirectories RCR01 to RCR10 (individual rat directories). Each rat directory contains the following NIfTI files:

o   bal.nii.gz and balsumcom.nii.gz : The separate acquisitions of the BSSFP experiment and the complex summation of the data respectively.

o   dtitot.nii.gz : The diffusion weighted volumes in the order that they were acquired.

o   bvals and bvecs : Text files containing the b-values and b-vectors in the order that they were acquired, so this corresponds with the dtitot.nii.gz file.

o   zerob: Text file containing the image numbers where images with no diffusion weighting were acquired.

o   ubal1.nii.gz, ubal2.nii.gz and ubal3.nii.gz : The three 3D spoiled gradient acquisitions with TE 15,10, and 5 ms respectively.

-       derivatives.zip : Zipped data directory ‘derivatives’ containing calculated images of the diffusion parameters after application of FMRIB’s diffusion toolbox DTIfit. In addition it contains a file dti3D_b0.nii.gz which is a summation of all the b0-images and a file mask.nii.gz containing the ‘brain’ mask used for application of DTIfit.

-       Sinke_BrainStructureFunction2018.pdf : The article based on (part) of these data.