Automatic quality control in clinical 1H MRSI of brain cancer
Pedrosa de Barros N, McKinley R, Knecht U, Wiest R, Slotboom J. NMR in Biomedicine 29(5):563-575, 2016.
References and acknowledgements
Citing spectrIm-QMRS
This page collects the most relevant publications for citing spectrIm-QMRS, its quality-control work, the TDFDFit fitting engine, and related MRS(I) methods developed in the Bern neuroimaging and MRS(I) research environment.
This reference list is a curated starting point. The PubMed entries below were verified during the website update on 29 June 2026. Please check the final journal formatting and decide which publications are required for a specific manuscript, dataset, or analysis pipeline.
Recommended citation logic
For publications that use spectrIm-QMRS as software, the most important spectrIm-QMRS application citation is the first Pedrosa de Barros and Slotboom quality-control paper listed below: Automatic quality control in clinical 1H MRSI of brain cancer. For work based on prior-knowledge model fitting, also cite the original TDFDFit paper. If the work uses SLOW-editing data or methods, cite the relevant SLOW-editing publications listed below.
When describing the software in a methods section, include the software name, version, and the fact that spectrIm-QMRS was used for MRS(I) visualization, preprocessing, modelling, fitting, quality control, or map generation as appropriate.
Core spectrIm-QMRS and quality-control references
These PubMed-verified papers involve Nuno Pedrosa de Barros and Johannes Slotboom and are relevant to spectrIm-QMRS quality management, MRSI quality control, and clinical brain tumor MRSI analysis workflows.
Quality management in in vivo proton MRS
Pedrosa de Barros N, Slotboom J. Analytical Biochemistry 529:98-116, 2017.
Improving labeling efficiency in automatic quality control of MRSI data
Pedrosa de Barros N, McKinley R, Wiest R, Slotboom J. Magnetic Resonance in Medicine 78(6):2399-2405, 2017.
Quality of clinical brain tumor MR spectra judged by humans and machine learning tools
Kyathanahally SP, Mocioiu V, Pedrosa de Barros N, Slotboom J, Wright AJ, Julia-Sape M, Arus C, Kreis R. Magnetic Resonance in Medicine 79(5):2500-2510, 2018.
On the relation between MR spectroscopy features and the distance to MRI-visible solid tumor in GBM patients
Pedrosa de Barros N, Meier R, Pletscher M, Stettler S, Knecht U, Herrmann E, Schucht P, Reyes M, Gralla J, Wiest R, Slotboom J. Magnetic Resonance in Medicine 80(6):2339-2355, 2018.
Analysis of metabolic abnormalities in high-grade glioma using MRSI and convex NMF
Pedrosa de Barros N, Meier R, Pletscher M, Stettler S, Knecht U, Reyes M, Gralla J, Wiest R, Slotboom J. NMR in Biomedicine 32(8):e4109, 2019.
TDFDFit references
Original TDFDFit paper
Slotboom J, Boesch C, Kreis R. Versatile frequency domain fitting using time domain models and prior knowledge. Magnetic Resonance in Medicine 39:899-911, 1998.
Basis-set composition and parameterization
Hofmann L, Slotboom J, Jung B, Maloca P, Boesch C, Kreis R. Quantitative 1H-magnetic resonance spectroscopy of human brain: influence of composition and parameterization of the basis set in linear combination model-fitting. Magnetic Resonance in Medicine, first published 23 August 2002.
Peer-reviewed SLOW-editing journal papers
The following PubMed-verified papers involve G. Weng and Johannes Slotboom and explicitly concern SLOW-editing or SLOW-editing based MRSI. These data were processed partially with spectrIm-QMRS.
SLOW: a novel spectral editing method for whole-brain MRSI at ultra high magnetic field
Weng G, Radojewski P, Sheriff S, Kiefer C, Schucht P, Wiest R, Maudsley AA, Slotboom J. Magnetic Resonance in Medicine 88(1):53-70, 2022.
Accurate prediction of IDH-mutation status of gliomas using SLOW-editing MRSI at 7T MR
Weng G, Ermis E, Maragkou T, Krcek R, Reinhardt P, Zubak I, Schucht P, Wiest R, Slotboom J, Radojewski P. Neuro-Oncology Advances 5(1):vdad001, 2023.
Simultaneous multi-region detection of GABA+ and Glx using 3D spatially resolved SLOW-editing and EPSI-readout at 7T
Weng G, Slotboom J, Schucht P, Ermis E, Wiest R, Kloppel S, Peter J, Zubak I, Radojewski P. NeuroImage 286:120511, 2024.
DOI: 10.1016/j.neuroimage.2024.120511 | PubMed PMID: 38184158 | HTML
To be checked manually: add local PDF download links if publication PDFs may legally be redistributed from this website. At present, the links point to DOI and PubMed publication pages.
Related journal papers and preprints
The following Weng/Slotboom-related publications and preprints are not listed above as peer-reviewed SLOW-editing journal papers, but may be relevant for users who work with modern MRSI acquisition, fitting, and analysis pipelines.
When More Is Less
Weng G, Slotboom J. When more is less: higher magnetic fields and their limited impact on signal-to-noise ratio per unit of acquisition time in unlocalized and single-voxel magnetic resonance spectroscopy. Physical Review Applied, 2025.
APS publication page | arXiv preprint | PDF
To be checked manually: confirm the final APS DOI string and final journal citation formatting from the publisher page.
TensorFit
Turco F, Capiglioni M, Weng G, Slotboom J. TensorFit: a torch-based tool for ultrafast metabolite fitting of large MRSI data sets. Magnetic Resonance in Medicine 92(2):447-458, 2024.
Deep learning quality filtering
Rakic M, Turco F, Weng G, Maes F, Sima DM, Slotboom J. Deep learning pipeline for quality filtering of MRSI spectra. NMR in Biomedicine 37(7):e5012, 2024.
alpha-D-Glucose as a non-radioactive MRS tracer
Weng G, Radojewski P, Slotboom J. alpha-D-Glucose as a non-radioactive MRS tracer for metabolic studies of the brain. Scientific Reports 13:6159, 2023.
DOI: 10.1038/s41598-023-33161-8 | PubMed PMID: 37061615 | PDF
CHEAP downfield 3D 1H-MRSI at 7T
CHEmical-shift selective Adiabatic Pulse (CHEAP): fast and high resolution downfield 3D 1H-MRSI at 7T. arXiv preprint, 2025.
To be checked manually: complete the author list and decide whether this related method paper belongs on the final spectrIm-QMRS citation page.
Conference abstracts and related supplied references
These entries were added from the supplied Google Scholar, ISMRM, and BORIS links. Several author lists are abbreviated in the source text, so the final author formatting should be checked manually before this section is treated as a formal bibliography.
SLOW whole-brain spectral editing EPSI using chemical selective adiabatic 2pi-refocusing pulses
ISMRM & SMRT Annual Meeting abstract, 2021. This abstract is connected with the development of whole-brain edited EPSI at ultra-high field and belongs to the SLOW-editing conference abstract trail rather than to the journal-paper list above.
To be checked manually: complete the author list and decide whether this abstract should be cited in manuscripts or kept as background documentation.
Simultaneous water and lipid suppression using chemical selective adiabatic refocusing pulses EPSI at 7T
ISMRM & SMRT Annual Meeting abstract, 2021. This work is related to chemical-shift displacement artifacts, B1 inhomogeneity, water and fat suppression, SAR limitations, and EPSI-based spectroscopy at 7T.
To be checked manually: complete author list and decide whether this abstract should be cited as a technical background reference for SLOW/CHEAP-related acquisition development.
CHEAP and SLOW: a comprehensive acquisition protocol for downfield, upfield, and spectral editing 1H-MRSI at 7T
Weng G, Radojewski P, Slotboom J. Proceedings of the ISMRM Annual Meeting, 2024. The abstract describes a combined CHEAP and SLOW acquisition protocol for downfield, upfield, and spectral-editing 1H-MRSI at 7T.
In vivo whole-brain downfield metabolites mapping using 2pi-CASP-EPSI at 7T
ISMRM & SMRT Annual Meeting abstract. The supplied reference connects this work with downfield MRSI and 7T EPSI-based acquisition.
To be checked manually: complete author list and year/journal conference formatting.
Clinical applicability of SLOW-editing compared to MEGA-editing for the evaluation of IDH-mutation status in glioma patients at 7T
Weng G, Slotboom J, Radojewski P. ISMRM & SMRT Annual Meeting abstract, 2022. This abstract compares SLOW-editing and MEGA-editing for 2HG detection in glioma-suspected patients at 7T.
Have a Coke and a Smile: sweet insights into brain glucose dynamics with SLOW-EPSI
ISMRM & ISMRT Annual Meeting abstract, 2025. The supplied BORIS entry links this work to non-invasive monitoring of glucose in the human brain.
To be checked manually: complete author list and add ISMRM archive link if available.
Clues from 1H MR spectroscopy about the cerebral micro-environment of ingested ethanol
ISMRM & ISMRT Annual Meeting abstract, 2025. The supplied BORIS entry links this work to MRS observations of cerebral ethanol.
To be checked manually: complete author list and decide whether this belongs on the final spectrIm-QMRS citation page.
Single-shot SLOW-editing for downfield alpha-glucose MRSI at 7T utilizing SNR-enhancing glucose mutarotation effect
Weng G, Radojewski P, Slotboom J. ISMRM abstract, 2023. This abstract is related to SLOW-editing for downfield alpha-glucose MRSI at 7T.
In vitro and in vivo SLOW-editing with 3D EPSI-readout at 3T: proof of principle
Weng G, Radojewski P, Sheriff S, Slotboom J. ISMRM abstract, 2024. This abstract extends the SLOW-editing concept to 3D EPSI-readout at 3T.
Simultaneous in vivo detection of cystathionine and 2HG at 7T and simulation of MEGA and SLOW-editing performance
Weng G, Radojewski P, Slotboom J. ISMRM abstract, 2023. This work concerns 2HG and cystathionine detection and simulation of MEGA and SLOW-editing performance.