MRSCloud: a Cloud-based MR Spectroscopy Tool for Basis Set Simulation

Hui, S. C. N.; Saleh, M.; Zoellner, H. J.; Oeltzschner, G.; Fan, H.; Li, Y.; Song, Y.; Jiang, H.; Near, J.; Lu, H.; Mori, S.; Edden, R.

doi:10.1101/2022.03.22.485310

bioRxiv · 10.1101/2022.03.22.485310

MRSCloud: a Cloud-based MR Spectroscopy Tool for Basis Set Simulation

Hui, S. C. N.·Saleh, M.·Zoellner, H. J.·Oeltzschner, G.·Fan, H.·Li, Y.·Song, Y.·Jiang, H.·Near, J.·Lu, H.·Mori, S.·Edden, R.

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Abstract

BackgroundAccurate quantification of in vivo proton magnetic resonance spectra involves modeling with a linear combination of known metabolite basis functions. Basis sets can be generated by numerical simulation using the quantum mechanical density-matrix formalism. Accurate simulations for a basis set require correct sequence timings, and pulse shapes and durations. PurposeTo present a cloud-based spectral simulation tool MRSCloud. It allows community users of MRS to simulate a vendor- and sequence-specific basis set online in a convenient and timeefficient manner. This tool can simulate basis sets for 3 major MR scanner vendors (GE, Philips, Siemens), including conventional acquisitions and spectral editing schemes (MEGA, HERMES, HERCULES) with PRESS and semi-LASER localization. Study TypeProspective. SpecimenN/A Field Strength/SequenceSimulations of 3T basis sets for conventional and spectral-editing sequences (MEGA, HERMES, HERCULES) with PRESS and sLASER localizations. AssessmentSimulated metabolite basis functions generated by MRSCloud are compared to those generated by FID-A and MARSS, and a phantom-acquired basis-set from LCModel. Statistical TestsIntraclass correlation coefficients (ICC) were calculated to measure the agreement between individual metabolite basis functions generated using different packages. Statistical analysis was performed using R in RStudio. ResultsSimulation time for a full basis set is approximately 1 hour. ICCs between MRSCloud and FID-A were at least 0.98 and ICCs between MRSCloud and MARSS were at least 0.96. ICCs between simulated MRSCloud basis spectra and acquired LCModel basis spectra were lowest for Gln at 0.68 and highest for NAA at 0.96. Data ConclusionSubstantial reductions in runtime have been achieved by implementing the 1D projection method, coherence-order filtering, and pre-calculation of propagators. High ICC values indicated that the accelerating features are running correctly and produce comparable and accurate basis sets. The generated basis set has been successfully used with LCModel.

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Hui, S. C. N., Saleh, M., Zoellner, H. J., Oeltzschner, G., Fan, H., Li, Y., Song, Y., Jiang, H., Near, J., Lu, H., Mori, S., Edden, R.. 2022-03-25. MRSCloud: a Cloud-based MR Spectroscopy Tool for Basis Set Simulation. https://doi.org/10.1101/2022.03.22.485310

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