This readme.txt file was generated on 2024-09-23 by Bernhard Strasser Recommended citation for the data: ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset 10.5 T CRT-MRSI metabolic, spectral and quality maps 2. Author Information Principal Investigator Contact Information Name: Malgorzata Marjanska Institution: University of Minnesota Department of Radiology Address: 2021 6th ST SE, , Minneapolis, Minnesota, United States of America Email: gosia@umn.edu ORCID: https://orcid.org/0000-0002-4727-2447 Associate or Co-investigator Contact Information Name: Wolfgang Bogner Institution: Medical University of Vienna Address: Lazarettgasse 14, BT 32, 1090 Vienna, Vienna, Austria Email: wolfgang.bogner@meduniwien.ac.at ORCID: 0000-0002-0130-3463 Associate or Co-investigator Contact Information Name: Lukas Hingerl Institution: Medical University of Vienna Address: Lazarettgasse 14, BT 32, 1090 Vienna, Vienna, Austria Email: lukas.hingerl@meduniwien.ac.at ORCID: 0000-0003-1808-8349 Associate or Co-investigator Contact Information Name: Bernhard Strasser Institution: Medical University of Vienna Address: Lazarettgasse 14, BT 32, 1090 Vienna, Vienna, Austria Email: bernhard.strasser@meduniwien.ac.at ORCID: 0000-0001-9542-3855 3. Date published or finalized for release: 2024-09-23 4. Date of data collection (single date, range, approximate date) 2023-12-01 to 2024-04-03 5. Geographic location of data collection (where was data collected?): University of Minnesota, Minneapolis, Minnesota, United States of America 6. Information about funding sources that supported the collection of the data: NIH: R01EB031787, P41 EB027061, P30 NS076408 Austrian Science Fund: WEAVE I 6037, P 34198, P 36328-N, KLI 1106 Christian Doppler Laboratory for MR Imaging Biomarkers (BIOMAK) 7. Overview of the data (abstract): These data show the metabolic maps, CRLB maps and LCModel fits, input data and fitted baseline in nifti-format of one volunteer measured at 10.5 Tesla. The volunteer was measured three different resolutions (4.40 mm³ isotropic, 3.44 mm³ isotropic, and 2.75 mm³ isotropic) using a concentric ring trajectory (CRT) FID-based sequence, reconstructed using a discrete Fourier transform, and fitted with LCModel (for more details, see below). The metabolic maps are in auxilliary units (a.u.) and are not in physical units. The uploaded metabolic maps contain the following metabolites (or sums thereof): aspartate, creatine + phosphocreatine, glucose, glutamate, glycerophosphocholine, glutathione, macromolecules, N-acetylaspartylglutamic acid, phosphocholine, scyllo-inositol, areatine, gamma aminobutyric acid, glutamine, glutamate + glutamine, glycerophosphocholine + phosphocholine, myo-inositol, N-acetylaspartate, N-acetylaspartate + N-acetylaspartylglutamic acid, phosphocreatine, taurine abbreviated as Asp_amp_map, Cr+PCr_amp_map, Glc_amp_map, Glu_amp_map, GPC_amp_map, GSH_amp_map, MMSim_amp_map, NAAG_amp_map, PCh_amp_map, Scyllo_amp_map, Cr_amp_map, GABA_amp_map, Gln_amp_map, Glu+Gln_amp_map, GPC+PCh_amp_map, Ins_amp_map, NAA_amp_map, NAA+NAAG_amp_map, PCr_amp_map, Tau_amp_map. The Cramer-Rao-Lower Bound (CRLB) maps of the same metabolites are named "[...]_sd_map" instead of "[...]_amp_map". The spectral maps contain the LCModel input spectra, fits and baseline fits as a time course (the x-axis is in fact chemical shift in ppm). Additional info is provided by the maps "0_pha_map.nii.gz", "1_pha_map.nii.gz", "SNR_map.nii.gz", "FWHM_map.nii.gz", "shift_map.nii.gz", "SNR_PseudoReplica_spectral_map.nii", "SNR_PseudoReplica_time_map.nii.gz", "FWHM_NAA_map.nii.gz", which are the zero- and first-order phase, SNR, FWHM, and spectral shifts as fitted by LCModel. The last three of these maps are the SNR in spectral and time domain, and the FWHM of NAA calculated by our own scripts. All these files can be viewed with freeview of freesurfer 7.1.1. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC BY 4.0 2. Links to publications that cite or use the data: not yet available - publication currently under review 3. Was data derived from another source? If yes, list source(s): No 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/policies/#drum-terms-of-use Yes. --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: Volunteer5_CRT_50x50x31 Short description: All metabolic maps, CRLB maps, quality-maps and spectral time courses fitted by LCModel for volunteer 5 with matrix size 50x50x31. B. Filename: Volunteer5_CRT_64x64x39 Short description: All metabolic maps, CRLB maps, quality-maps and spectral time courses fitted by LCModel for volunteer 5 with matrix size 64x64x39. C. Filename: Volunteer5_CRT_80x80x49 Short description: All metabolic maps, CRLB maps, quality-maps and spectral time courses fitted by LCModel for volunteer 5 with matrix size 80x80x49. All above contain the following files: Asp_amp_map.nii.gz, Cr+PCr_amp_map.nii.gz, Glc_amp_map.nii.gz, Glu_amp_map.nii.gz, GPC_amp_map.nii.gz, GSH_amp_map.nii.gz, MMSim_amp_map.nii.gz, NAAG_amp_map.nii.gz, PCh_amp_map.nii.gz, Scyllo_amp_map.nii.gz, Cr_amp_map.nii.gz, GABA_amp_map.nii.gz, Gln_amp_map.nii.gz, Glu+Gln_amp_map.nii.gz, GPC+PCh_amp_map.nii.gz, Ins_amp_map.nii.gz, NAA_amp_map.nii.gz, NAA+NAAG_amp_map.nii.gz, PCr_amp_map.nii.gz, Tau_amp_map.nii.gz, Asp_sd_map.nii.gz, Cr+PCr_sd_map.nii.gz, Glc_sd_map.nii.gz, Glu_sd_map.nii.gz, GPC_sd_map.nii.gz, GSH_sd_map.nii.gz, MMSim_sd_map.nii.gz, NAAG_sd_map.nii.gz, PCh_sd_map.nii.gz, Scyllo_sd_map.nii.gz, Cr_sd_map.nii.gz, GABA_sd_map.nii.gz, Gln_sd_map.nii.gz, Glu+Gln_sd_map.nii.gz, GPC+PCh_sd_map.nii.gz, Ins_sd_map.nii.gz, NAA_sd_map.nii.gz, NAA+NAAG_sd_map.nii.gz, PCr_sd_map.nii.gz, Tau_sd_map.nii.gz, SpecMap_LCMBaseline.nii.gz, SpecMap_LCMFit.nii.gz, SpecMap_LCMInput.nii.gz, 0_pha_map.nii.gz, 1_pha_map.nii.gz, SNR_map.nii.gz, FWHM_map.nii.gz, shift_map.nii.gz, SNR_PseudoReplica_spectral_map.nii, SNR_PseudoReplica_time_map.nii.gz, FWHM_NAA_map.nii.gz 2. Relationship between files: A,B,C are from the same volunteer, but different resolutions. Different maps (metabolites, CRLBs, quality and spectral maps) -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Volunteer 5 was measured with three different resolutions (4.40 mm³ isotropic, 3.44 mm³ isotropic, and 2.75 mm³ isotropic) using a concentric ring trajectory (CRT) FID-based sequence with the following parameters: - Matrix size 50×50×31, field-of-view (FOV) 220×220×136 mm³, SBW 4000 Hz, TR 450 ms, nominal flip angle 45°, readout duration 307 ms, acquisition duration 10:27 min:s, up to 3 variable TIs (center partition: 1 TI: 3 rings, 2 TIs: 8 rings, 3 TIs: 14 rings, total 1387 TRs , all five volunteers ) - Matrix size 64×64×39, FOV 220×220×136 mm³, SBW 3705 Hz, TR 320 ms, nominal flip angle 35°, readout duration 207 ms, acquisition duration 15:05 min:s, up to 4 variable TIs (center partition: 1 TI: 3 rings, 2 TIs: 10 rings, 4TIs: 19 rings, total 2819 TRs, all five volunteers ) - Matrix size 80×80×49, FOV 220×220×139 mm³, SBW 3705 Hz, TR 320 ms, nominal flip angle 35°, readout duration 207 ms, acquisition duration 25:22 min:s, up to 4 variable TIs (center partition: 1TI: 3 rings, 2 TIs: 10 rings, 4 TIs: 27 rings, total 4749 TRs, two volunteers) 2. Methods for processing the data: The reconstruction consisted of the following steps, performed offline in MATLAB: - Channel-wise noise decorrelation - Off-resonance (due to chemical shift) correction for the different k-space points on the rings each having its own time delay - Correcting in-plane FOV shifts - k-Space density correction to achieve a 3D Hamming filter - Fourier transformation along the kx-ky-directions with a discrete Fourier operator - Fourier transformation along z-direction with the FFT algorithm - Coil- and slice-wise lipid decontamination via L2-regularization - Coil combination using the interleaved iMUSICAL calibration data. The fitting was performed with LCModel using a basis set containing 17 different metabolite spectra simulated using NMRScopeB and simulated macromolecular signals based on known resonance positions, and relaxation times as described in doi: 10.1016/j.neuroimage.2022.119574. A first-order phase error was introduced to the basis set by truncating the initial part of the FIDs to match the measured data. The LCModel fitting provides a metabolic concentration map ("[...]_amp_map"), and an uncertainty map in the form of a relative CRLB map in percent ("[...]_sd_map") for each metabolite. 3. Instrument- or software-specific information needed to interpret the data: All files are in nifti format and can be viewed with freeview of freesurfer 7.1.1. 4. Standards and calibration information, if appropriate: Nifti standard. The metabolic maps are not calibrated, i.e. the maps are in auxilliary units, and NOT in mmol/l. The CRLBs are in percent relative to the metabolic amplitudes. 5. Environmental/experimental conditions: Data obtained from healthy human brain. 6. Describe any quality-assurance procedures performed on the data: We removed outliers in the metabolic maps where the values were 13 times the median absolute deviation away from the median. 7. People involved with sample collection, processing, analysis and/or submission: Lukas Hingerl, Bernhard Strasser, Simon Schmidt, Korbinian Eckstein, Guglielmo Genovese, Edward J. Auerbach, Andrea Grant, Matt Waks, Philipp Lazen, Alireza Sadeghi-Tarakameh, Gilbert Hangel, Fabian Niess, Yigitcan Eryaman, Gregor Adriany, Gregory Metzger, Andrew Wright, Wolfgang Bogner, Małgorzata Marjańska ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Volunteer5_CRT_50x50x31 ----------------------------------------- 1. Number of variables: 3 or 4 (3 for metabolic maps, CRLB maps, quality maps. 4 for SpecMap_LCMBaseline.nii.gz, SpecMap_LCMInput.nii.gz, SpecMap_LCMFit.nii.gz) 2. Number of cases/rows: N/A 3. Missing data codes: Code/symbol NaN 4. Variable List A. Name: x Description: Spatial coordinate x [mm] B. Name: y Description: Spatial coordinate y [mm] C. Name: z Description: Spatial coordinate z [mm] D. Name: ChemicalShift (only for SpecMap_LCMBaseline.nii.gz, SpecMap_LCMInput.nii.gz, SpecMap_LCMFit.nii.gz) Description: Chemical shift [ppm] ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Volunteer5_CRT_64x64x39 ----------------------------------------- 1. Number of variables: 3 or 4 (3 for metabolic maps, CRLB maps, quality maps. 4 for SpecMap_LCMBaseline.nii.gz, SpecMap_LCMInput.nii.gz, SpecMap_LCMFit.nii.gz) 2. Number of cases/rows: N/A 3. Missing data codes: Code/symbol NaN 4. Variable List A. Name: x Description: Spatial coordinate x [mm] B. Name: y Description: Spatial coordinate y [mm] C. Name: z Description: Spatial coordinate z [mm] D. Name: ChemicalShift (only for SpecMap_LCMBaseline.nii.gz, SpecMap_LCMInput.nii.gz, SpecMap_LCMFit.nii.gz) Description: Chemical shift [ppm] ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Volunteer5_CRT_80x80x49 ----------------------------------------- 1. Number of variables: 3 or 4 (3 for metabolic maps, CRLB maps, quality maps. 4 for SpecMap_LCMBaseline.nii.gz, SpecMap_LCMInput.nii.gz, SpecMap_LCMFit.nii.gz) 2. Number of cases/rows: N/A 3. Missing data codes: Code/symbol NaN 4. Variable List A. Name: x Description: Spatial coordinate x [mm] B. Name: y Description: Spatial coordinate y [mm] C. Name: z Description: Spatial coordinate z [mm] D. Name: ChemicalShift (only for SpecMap_LCMBaseline.nii.gz, SpecMap_LCMInput.nii.gz, SpecMap_LCMFit.nii.gz) Description: Chemical shift [ppm]