Published December 19, 2024
| Version v1
Dataset
Open
Open Data Repository - 2-deoxy-D-glucose chemical exchange-sensitive spin-lock MRI of cerebral metabolism after stroke in the rat
Authors/Creators
- 1. Charité-Universitätsmedizin Berlin, Center for Stroke Research Berlin, Charitéplatz 1, 10117 Berlin, Germany
- 2. Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental Imaging at the Charité for 3R (EPIC3R), Charité 3R – Replace | Reduce | Refine, Berlin, Germany
- 3. Charité-Universitätsmedizin Berlin, Department of Neurology with Experimental Neurology, Berlin, Germany
- 4. Charité-Universitätsmedizin Berlin, Department of Radiology, Berlin, Germany
- 5. Physikalisch-Technische Bundesanstalt (PTB), Braunschweig and Berlin, Germany
- 6. The University of Newcastle, Australia
- 7. University of Oxford, Radcliffe Department of Medicine, Oxford, United Kingdom
- 8. Consortium International pour la Recherche Circadienne sur l'AVC (CIRCA)
- 9. University of Oxford, Nuffield Department of Clinical Neurosciences, Oxford, United Kingdom
- 10. German Cancer Research Center, Translational Molecular Imaging, Heidelberg, Germany
- 11. Ruprecht Karls University Heidelberg, Department for Physics and Astronomy, Heidelberg, Germany
- 12. German Cancer Consortium (DKTK), Heidelberg, Germany
Description
This dataset contains in vivo MRI data of rats after 90 min proximal MCAO
Other
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
Last updated: 2024/12/18
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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
Files
dat.zip
Additional details
Dates
- Submitted
-
2025-01-07v1 for biorxiv preprint