---
title: "MRSIPrep: Standardized Post-Quantification Pipeline for Whole-Brain MRSI"
id: "biorxiv-22-mrsiprep-a-standardized-post-quantification-framework-for-preprocessing-whole"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-22-mrsiprep-a-standardized-post-quantification-framework-for-preprocessing-whole"
content_type: "clinical_feed_article"
specialty: "Radiology"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.09.11.750896v1?rss=1"
published_at: "2026-09-16T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# MRSIPrep: Standardized Post-Quantification Pipeline for Whole-Brain MRSI
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-22-mrsiprep-a-standardized-post-quantification-framework-for-preprocessing-whole
- **Specialty:** [Radiology](https://medichelpline.com/clinical-feed/radiology.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.09.11.750896v1?rss=1)
- **Published At:** 2026-09-16T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- **MRSIPrep** is an open-source, modular, reproducible post-quantification framework designed for whole-brain **magnetic resonance spectroscopic imaging (MRSI)** data. - The tool addresses heterogeneity in downstream processing of quantified metabolite maps across laboratories by standardizing key steps after spectral fitting and quantification. - Core processing steps include automated **quality control**, **tissue correction**, **spatial normalization**, **atlas projection**, and derivative generation from metabolite maps and associated quality metrics. - Outputs are produced at voxelwise and regional levels and are formatted to be **connectomics-ready**, facilitating downstream network and regional analyses. - MRSIPrep generates automated quality-control reports to support reproducible and transparent MRSI analysis. - The framework is modular and intended to work across diverse datasets, acquisition protocols, and downstream applications; the authors demonstrated its utility for reproducible MRSI analysis across such variability. - The project is available publicly with source code on GitHub and documentation online (links provided in the preprint). - The work is presented as a preprint and has not been peer reviewed; competing interest: one author is employed by Siemens Healthcare and other authors declared no competing interests. - Funding sources reported include the Swiss National Science Foundation and several foundations; code and documentation repositories are provided for community use and transparency.
## Clinical Analysis & Structured Key Points
MRSIPrep: A Standardized Post-Quantification Framework for Preprocessing Whole-Brain Magnetic Resonance Spectroscopic Imaging | bioRxiv Skip to main content New Results MRSIPrep: A Standardized Post-Quantification Framework for Preprocessing Whole-Brain Magnetic Resonance Spectroscopic Imaging View ORCID Profile Federico Lucchetti , View ORCID Profile Edgar Celereau , View ORCID Profile Raoul Jenni , View ORCID Profile Jean-Baptiste Ledoux , View ORCID Profile Stephan Eliez , View ORCID Profile Farnaz Delavari , View ORCID Profile Patric Hagmann , View ORCID Profile Yasser Aleman-Gomez , View ORCID Profile Antoine Klauser , View ORCID Profile Paul Klauser doi: https://doi.org/10.64898/2026.09.11.750896 Federico Lucchetti 1 Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Federico Lucchetti Edgar Celereau 1 Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Edgar Celereau Raoul Jenni 1 Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Raoul Jenni Jean-Baptiste Ledoux 1 Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Jean-Baptiste Ledoux Stephan Eliez 2 Developmental Imaging and Psychopathology Laboratory, Department of Psychiatry, University of Geneva School of Medicine, Geneva, Switzerland; Department of Genetic Medicine and Development, University of Geneva School of Medicine, Geneva, Switzerland; Fon; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Stephan Eliez Farnaz Delavari 3 Department of Radiology, Lausanne University Hospital, Lausanne, Switzerland; Developmental Imaging and Psychopathology Laboratory, Department of Psychiatry, University of Geneva School of Medicine, Geneva, Switzerland; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Farnaz Delavari Patric Hagmann 4 Department of Radiology, Lausanne University Hospital, Lausanne, Switzerland; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Patric Hagmann Yasser Aleman-Gomez 4 Department of Radiology, Lausanne University Hospital, Lausanne, Switzerland; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Yasser Aleman-Gomez Antoine Klauser 5 Swiss Innovation Hub, Siemens Healthineers International AG, Lausanne, Switzerland; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Antoine Klauser Paul Klauser 6 Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland; Division of Child and Adolescent Psychiatry, Department of Psychiatry, Lausanne University Hospital and Universi Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Paul Klauser For correspondence: paul.klauser{at}unil.ch Abstract Info/History Metrics Data/Code Preview PDF Abstract Magnetic resonance spectroscopic imaging (MRSI) enables non-invasive mapping of neu-rometabolites levels across the human brain. Although spectral fitting and metabolite quan-tification are increasingly supported by mature software tools, the downstream processing of quantified metabolite maps remains heterogeneous across laboratories. Here, we introduce MRSIPrep, an open-source, modular, and reproducible post-quantification framework for whole-brain MRSI. MRSIPrep standardizes quality control, tissue correction, spatial nor- malization, atlas projection, and derivative generation from quantified metabolite maps and associated quality metrics. The framework produces voxelwise, regional, and connectomics-ready outputs together with automated quality-control reports. We describe the architecture of MRSIPrep and demonstrate its utility for reproducible MRSI analysis across datasets,acquisition protocols, and downstream applications. Competing Interest Statement Antoine Klauser is employed by Siemens Healthcare as a research scientist. He contributes to on-site research and development initiatives. He does not hold fiduciary responsibilities for Siemens Healthcare. All the other authors declare no competing interests. Footnotes https://github.com/MRSI-Psychosis-UP/MRSIPrep https://mrsiprep.readthedocs.io/en/stable/ Funder Information Declared Swiss National Science Foundation , 320030_144260 , 320030_179404 , 320030_212476 NeuroNA foundation The Copley May foundation Synapsy Center Fondation Pôle Autisme Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license . Back to top Previous Next Posted September 16, 2026. Download PDF Data/Code Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. 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Share MRSIPrep: A Standardized Post-Quantification Framework for Preprocessing Whole-Brain Magnetic Resonance Spectroscopic Imaging Federico Lucchetti , Edgar Celereau , Raoul Jenni , Jean-Baptiste Ledoux , Stephan Eliez , Farnaz Delavari , Patric Hagmann , Yasser Aleman-Gomez , Antoine Klauser , Paul Klauser bioRxiv 2026.09.11.750896; doi: https://doi.org/10.64898/2026.09.11.750896 Share This Article: Copy Citation Tools MRSIPrep: A Standardized Post-Quantification Framework for Preprocessing Whole-Brain Magnetic Resonance Spectroscopic Imaging Federico Lucchetti , Edgar Celereau , Raoul Jenni , Jean-Baptiste Ledoux , Stephan Eliez , Farnaz Delavari , Patric Hagmann , Yasser Aleman-Gomez , Antoine Klauser , Paul Klauser bioRxiv 2026.09.11.750896; doi: https://doi.org/10.64898/2026.09.11.750896 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Areas All Articles Animal Behavior and Cognition (8003) Biochemistry (18709) Bioengineering (14839) Bioinformatics (44356) Biophysics (22557) Cancer Biology (19680) Cell Biology (26844) Clinical Trials (138) Developmental Biology (13942) Ecology (20969) Epidemiology (2067) Evolutionary Biology (25412) Genetics (16150) Genomics (23476) Immunology (18677) Microbiology (42397) Molecular Biology (18020) Neuroscience (93337) Paleontology (699) Pathology (2977) Pharmacology and Toxicology (5085) Physiology (8105) Plant Biology (15969) Scientific Communication and Education (2094) Synthetic Biology (4549) Systems Biology (10219) Zoology (2384)
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