Magnetic resonance spectroscopy data for GABA quantification using MEGAPRESS pulse sequence

Magnetic resonance spectroscopy data for GABA quantification using MEGAPRESS pulse sequence

Citation Author(s):
S.M.
Shermer
Department of Physics at Swansea University, Swansea, UK
C.
Jenkins
CUBRIC at Cardiff University, Cardiff, UK
M.
Chandler
School of Computer Science and Informatics, Cardiff University, Cardiff, UK
F. C.
Langbein
School of Computer Science and Informatics, Cardiff University, Cardiff, UK
Submitted by:
Frank Langbein
Last updated:
Fri, 08/16/2019 - 13:54
DOI:
10.21227/ak1d-3s20
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License:
Creative Commons Attribution
Dataset Views:
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Magnetic resonance spectroscopy (MRS) data for a series of GABA phantoms specifically  designed to provide ground truth data for GABA quantification based on MRS data. The spectra were obtained using the WIP Siemens implementation svs-edit of the common edited spectroscopy MEGAPRESS sequence on a 3T Siemens Magnetom Skyra system installed in the Clinical Imaging Unit at Swansea University (UK).

Instructions: 

The dataset consists of MRS data for four different phantoms.

* E1 - pH-calibrated solutions of NAA, CRE and varying amounts of GABA scanned at room temperature.
* E2 - non-pH calibrated solutions of NAA, CRE and varying amounts of GABA scanned at room temperature.
* E3 - pH calibrated solutions of NAA, CRE, GLU, GLN and varying amounts of GABA scanned at room temperature.
* E4 - pH calibrated gel phantoms containing NAA, CRE, GLU, GLU and various amounts of GABA.

The preparation of the phantoms is detailed in readme-phantoms.md and the composition of the phantoms for each experiment is detailed in the spreadsheet phantoms.ods. The gel phantoms (E4) were scanned 4 times on two different dates with two different acquisition bandwidths leading to four datasets E4a, E4b, E4c, E4d.

Each of the top-level directory has multiple sub-directories, e.g., for E1:

* MEGA_Combi_WS_ON: averaged MEGAPRESS spectra in Siemens spectroscopy dicom (.IMA) format;
* MEGA_SingleAve_WS_ON: single average MEGAPRESS spectra in Siemens spectroscopy dicom (.IMA) format;
* PRESS_WS_OFF: water-unsuppressed spectra (in this case PRESS spectra);
* RAW: raw spectroscopy data in Siemens .dat format.

Each of these subdirectories in turn contains several subdirectories for each experiment performed, e.g., ls E1/MEGA_Combi_WS_ON gives

* GABA00_NAA_15mM_Cr_0mM,
* GABA04_NAA_15mM_Cr_8mM,
* GABA09_NAA_15mM_Cr_8mM,
* GABA00_NAA_15mM_Cr_8mM,
* GABA05_NAA_15mM_Cr_8mM,
* GABA10_NAA_15mM_Cr_8mM,
* GABA01_NAA_15mM_Cr_8mM,
* GABA06_NAA_15mM_Cr_8mM,
* GABA11_NAA_15mM_Cr_8mM,
* GABA02_NAA_15mM_Cr_8mM,
* GABA07_NAA_15mM_Cr_8mM,
* GABA03_NAA_15mM_Cr_8mM,
* GABA08_NAA_15mM_Cr_8mM.

For the combined spectra, each of these subdirectories contains 3 IMA files

* MP_EDIT_DIFF.IMA: MEGAPRESS EDIT DIFF spectrum;
* MP_EDIT_OFF.IMA: MEGAPRESS EDIT OFF spectrum;
* MP_EDIT_ON.IMA: MEGAPRESS EDIT ON spectrum.

The full scan protocols are embedded in the IMA files.

For the single average MEGAPRESS spectra, each subdirectory contains 320 IMA files named 0001.IMA to 0320.IMA where the odd numbered spectra are MP EDIT ON spectra and the even numbered spectra are EDIT OFF.

Each subdirectory in the RAW directory will usually contain two .dat files, one corresponding to water suppressed and one water unsuppressed. Which is which is clear from the file names where svs_edit indicates MEGAPRESS scans and svs_se corresponds to the standard PRESS sequence. The spreadsheet calibration.ods also links the scan numbers and the corresponding measurements ID and acquisition times. WS_OFF indicates that the scan was performed with water suppression turned OFF. The default is WS ON. In some cases additional information is provided, e.g., a warning if any auto-adjustments between the two scans were detected.

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[1] , "Magnetic resonance spectroscopy data for GABA quantification using MEGAPRESS pulse sequence", IEEE Dataport, 2019. [Online]. Available: http://dx.doi.org/10.21227/ak1d-3s20. Accessed: Oct. 16, 2019.
@data{ak1d-3s20-19,
doi = {10.21227/ak1d-3s20},
url = {http://dx.doi.org/10.21227/ak1d-3s20},
author = { },
publisher = {IEEE Dataport},
title = {Magnetic resonance spectroscopy data for GABA quantification using MEGAPRESS pulse sequence},
year = {2019} }
TY - DATA
T1 - Magnetic resonance spectroscopy data for GABA quantification using MEGAPRESS pulse sequence
AU -
PY - 2019
PB - IEEE Dataport
UR - 10.21227/ak1d-3s20
ER -
. (2019). Magnetic resonance spectroscopy data for GABA quantification using MEGAPRESS pulse sequence. IEEE Dataport. http://dx.doi.org/10.21227/ak1d-3s20
, 2019. Magnetic resonance spectroscopy data for GABA quantification using MEGAPRESS pulse sequence. Available at: http://dx.doi.org/10.21227/ak1d-3s20.
. (2019). "Magnetic resonance spectroscopy data for GABA quantification using MEGAPRESS pulse sequence." Web.
1. . Magnetic resonance spectroscopy data for GABA quantification using MEGAPRESS pulse sequence [Internet]. IEEE Dataport; 2019. Available from : http://dx.doi.org/10.21227/ak1d-3s20
. "Magnetic resonance spectroscopy data for GABA quantification using MEGAPRESS pulse sequence." doi: 10.21227/ak1d-3s20