DOI: 10.5281/zenodo.14526091
title: Open Data Repository - 2-deoxy-D-glucose chemical exchange-sensitive spin-lock MRI of cerebral metabolism after stroke in the rat

description: This dataset contains in vivo MRI data of rats after 90 min proximal MCAO from the study published here: https://doi.org/10.1177/0271678X251355049
description: Manuscript information

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2-Deoxy-D-Glucose chemical exchange-sensitive spin-lock MRI of cerebral metabolism after stroke in the rat

 

Authors: Philipp Boehm-Sturm, Patrick Schuenke, Marco Foddis, Susanne Mueller, Stefan P. Koch, Daniel J. Beard,

Paul Holloway, Amin Mottahedin, Leif Schröder, Alastair M. Buchan, Philipp Mergenthaler

 

Preprint: https://doi.org/10.1101/2025.01.08.628135

 

Paper: https://doi.org/10.1177/0271678X251355049

 

Last updated: 2025/07/10

 

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Contact

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PD Dr. Philipp Mergenthaler

Charité-Universitätsmedizin Berlin, 

Department of Neurology with Experimental Neurology and Center for Stroke Research

Charitéplatz 1, 10117 Berlin, Germany

email: philipp.mergenthaler@charite.de

 

Prof. Dr. Philipp Boehm-Sturm

Charité-Universitätsmedizin Berlin, 

Charité 3R - Replace|Reduce|Refine, Department of Experimental Neurology and Center for Stroke Research 

Charitéplatz 1, 10117 Berlin, Germany

email: philipp.boehm-sturm@charite.de

 

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Description

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This dataset contains in vivo MRI data of rats after 90 min proximal MCAO

 

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Folder and subfolder names

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dat - directory containing processed datasets including ANTx2 (https://github.com/ChariteExpMri/antx2) project file

- All subdirectories (MRI IDs) follow the follwing name structure: 

  [ExperimentDate]_[InitialsExperimenter]_[GroupNumber]_[SubjectNumber] e.g. 20200716SA_G1_D7

 

raw - directory containing Bruker raw data, documentation of individual scans in documentation_scan_numbers_rawData.xlsx

 

code - directory containing scripts for processing the data with ANTx2/MATLAB

 

results - directory containing statistic results

 

templates - directory containing the SIGMA rat brain template and atlas used for processing

 

 

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List of files

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README.txt - (this file)

documentation_scan_numbers_rawData.xlsx - assignment of scan numbers

 

dat directory also contains many intermediate files, only important ones are documented here:

 

t2.nii / x_t2.nii t2 weighted MRI in the native (raw data) / atlas space

 

07_DWI_Trace_EPI_sat_XX_1.nii  diffusion MRI raw data

 

08_Perfusion_FAIR_EPI_studyShim_XX_1.nii Perfusion MRI raw data

 

 

 

T1rho_2DG__001.nii CESL MRI raw data containing 13 spin lock frames

 

c_c_T1rho_2DG__001.nii Motion corrected CESL MRI raw data, i.e. registered to the first CESL scan, used for calculating R1rho maps

 

c_CBF_CBFcorrected_slice.nii Calculated CBF map in registration with R1rho maps

c_ADC_ADC_slice.nii Calculated ADC map in registration with R1rho maps

 

mean_R1rho_001-005.nii baseline R1rho map used for calculating deltaR1rho

mean_R1rho_031-035.nii late R1rho map used for segmenting the metabolic lesion and for quantitative analyses

 

deltaR1rho_i.nii; i=001-035 calculated delta R1rho maps, coregistered to the first T1rho images

 

mask_Core__fromADC.nii mask of lesion core from ADC, registered to R1rho maps

mask_Core__fromADC_mirror.nii mask of lesion core from ADC, registered to R1rho maps and mirrored at midline in atlas space, then backtransformed

 

mask_Hypoperfused__fromCBF.nii mask of hypoperfused area from CBF, registered to R1rho maps

mask_Hypoperfused__fromCBF_mirror.nii mask of hypoperfused area from CBF, registered to R1rho maps, registered to R1rho maps and mirrored at midline in atlas space, then backtransformed

 

mask_Penumbra.nii mask of penumbra (mismatch of the above)

mask_Penumbra_mirror.nii mask of penumbra (mismatch of the above), mirrored at midline in atlas space, then backtransformed