Description

This library provides extensive functionality to reconstruct magnetic resonance spectroscopy data. These include:

1. preprocess raw data including:
   • metabolite cycling
   • frequency alignment both in time and frequency domain
   • Averaging
   • Eddy current correction
   • coil combination
   • HSVD water suppression
   • etc. See functions such as reconstruct, reconstruct_all_...
2. call LCModel spectral fitting via ssh
3. calculate mmol/kg concentrations
4. all above functionalities are adapted to:
   • upfield spectra
   • downfield spectra
   • macromolecular spectra
   • macromolecular spectra fitted to amino acids models
   • creating and evaluating simulated spectra
   • functional MRS data

Dependencies

For reading in raw scanner data files, the mapVBVD function by Philipp Ehses was used. This and other functions to read in raw scanner data can be found in the Gannet2.0 repository: https://github.com/cjohnevans/Gannet2.0 Additional MATLAB packages used by the code include: https://de.mathworks.com/matlabcentral/fileexchange/27999-ssh-from-matlab-updated-sftp-scp https://de.mathworks.com/matlabcentral/fileexchange/19729-passwordentrydialog https://de.mathworks.com/matlabcentral/fileexchange/27418-fdr_bh https://de.mathworks.com/matlabcentral/fileexchange/28303-bonferroni-holm-correction-for-multiple-comparisons https://de.mathworks.com/matlabcentral/fileexchange/71052-blandaltmanplot https://de.mathworks.com/matlabcentral/fileexchange/13634-axescoord2figurecoord https://de.mathworks.com/matlabcentral/fileexchange/5782-eps2pdf

Publications

Following noteable publications used this library:

Giapitzakis, I. A., Shao, T., Avdievich, N., Mekle, R., Kreis, R., & Henning, A. (2018). Metabolite‐cycled STEAM and semi‐LASER localization for MR spectroscopy of the human brain at 9.4 T. Magnetic resonance in medicine, 79(4), 1841-1850.

Giapitzakis, I. A., Borbath, T., Murali‐Manohar, S., Avdievich, N., & Henning, A. (2019). Investigation of the influence of macromolecules and spline baseline in the fitting model of human brain spectra at 9.4 T. Magnetic resonance in medicine, 81(2), 746-758.

Giapitzakis, I. A., Avdievich, N., & Henning, A. (2018). Characterization of macromolecular baseline of human brain using metabolite cycled semi‐LASER at 9.4 T. Magnetic resonance in medicine, 80(2), 462-473.

Avdievich, N. I., Giapitzakis, I. A., Pfrommer, A., Borbath, T., & Henning, A. (2018). Combination of surface and ‘vertical’loop elements improves receive performance of a human head transceiver array at 9.4 T. NMR in Biomedicine, 31(2), e3878.

Murali‐Manohar, S., Borbath, T., Wright, A. M., Soher, B., Mekle, R., & Henning, A. (2020). T2 relaxation times of macromolecules and metabolites in the human brain at 9.4 T. Magnetic resonance in medicine, 84(2), 542-558.

Murali‐Manohar, S., Wright, A. M., Borbath, T., Avdievich, N. I., & Henning, A. (2021). A novel method to measure T1‐relaxation times of macromolecules and quantification of the macromolecular resonances. Magnetic resonance in medicine, 85(2), 601-614.

Borbath, T., Murali‐Manohar, S., Wright, A. M., & Henning, A. (2021). In vivo characterization of downfield peaks at 9.4 T: T2 relaxation times, quantification, pH estimation, and assignments. Magnetic resonance in medicine, 85(2), 587-600.

Dorst, J., Ruhm, L., Avdievich, N., Bogner, W., & Henning, A. (2021). Comparison of four 31P single‐voxel MRS sequences in the human brain at 9.4 T. Magnetic resonance in medicine, 85(6), 3010-3026.

Borbath, T., Murali‐Manohar, S., Dorst, J., Wright, A. M., & Henning, A. (2021). ProFit‐1D—A 1D fitting software and open‐source validation data sets. Magnetic resonance in medicine