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Reproducibility Made Easy: A Tool for Methodological Transparency and Efficient Standardized Reporting based on the proposed MRSinMRS Consensus.
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Antonia Susnjar1, Antonia Kaiser2, Dunja Simicic5,6, Gianna Nossa3, Alexander Lin4,Georg Oeltzschner5,6, Aaron Gudmundson5,6,71) Athinoula A. Martinos Center for Biomedical Imaging, Institute for Innovation in Imaging,Department of Radiology Massachusetts General Hospital and Harvard Medical School, BostonMA.2) CIBM Center for Biomedical Imaging, École polytechnique fédérale de Lausanne (EPFL),Lausanne, Switzerland3) School of Health Sciences, Purdue University, West Lafayette, IN, USA4) Center for Clinical Spectroscopy, Department of Radiology, Brigham and Women's Hospital,Harvard Medical School, Boston, MA.5) Russell H. Morgan Department of Radiology and Radiological Science, The Johns HopkinsUniversity School of Medicine, Baltimore, MD.6) F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute,Baltimore, MD.7) The Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore MD.* authors have contributed equallyAbstractPurpose:Recent expert consensus publications have highlighted the issue of poor reproducibility inmagnetic resonance spectroscopy (MRS) studies, mainly due to the lack of standardizedreporting criteria, which affects their clinical applicability. To combat this, guidelines for minimumreporting standards (MRSinMRS) were introduced to aid journal editors and reviewers inensuring the comprehensive documentation of essential MRS study parameters. Despite theseefforts, the implementation of MRSinMRS standards has been slow, attributed to the diversenomenclature used by different vendors, the variety of raw MRS data formats, and the absenceof appropriate software tools for identifying and reporting necessary parameters. To overcomethis obstacle, we have developed the REproducibility Made Easy (REMY) standalone toolbox.Methods:REMY software supports a range of MRS data formats from major vendors like GE (p. file),Siemens (.twix, .rda, .dcm), Philips (.spar/.sdat), and Bruker (.method), facilitating easy dataimport and export through a user-friendly interface. REMY employs external libraries such asspec2nii and pymapVBVD to accurately read and process these diverse data formats, ensuringcompatibility and ease of use for researchers in generating reproducible MRS research outputs.Users can select and import datasets, choose the appropriate vendor and data format, and thengenerate an MRSinMRS table, log file, and methodological documents in both Latex and PDFformats.Results:REMY effectively populated key sections of the MRSinMRS table with data from all supportedfile types. In the hardware section, it successfully read and filled in fields for Field Strength [T],Manufacturer Name, and Software Version, covering three of the five required hardware fields.However, it could not input data for RF coil and additional hardware information due to theirabsence in the files. For the acquisition section, REMY accurately read and populated fields forthe pulse sequence name, nominal voxel size, repetition time, echo time, number ofacquisitions/excitations/shots, spectral width [Hz], and number of spectral points, significantlycontributing to the completion of the Acquisition fields of the table. Furthermore, REMYgenerates a boilerplate methods text section for manuscripts.Conclusion:This approach reduces effort and obstacles associated with writing and reporting acquisitionparameters and should lead to the widespread adoption of MRSinMRS within the MRScommunity.Abbreviations: MRS, MRSinMRS, ReproducibilityMadeEasy

GE pfiles (.7) 19 GE pfiles (.7) were tested, ranging from software versions HD16 to MR24. The application was 100% successful in reading in all 19 datasets. It was 91.6% successful in
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6% successful extracting the aimed parameters, extracting all the aimed parameters except the scanner model for 14 datasets (which is not available for this file type) and 83% successful for 5 datasets by failing to extract the number of spectral points in addition to the model. It's important to emphasize that the application reads GE pfiles for version 7 onwards, as supported by spec2nii since the parameter notation is drastically different in files before that version.
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Bruker method files 2 Bruker datasets were tested. The application was 100% successful in extracting the aimed parameters for these datasets, except for the scanner model information, which is inaccessible from this file type, leading to 91.6 % overall success rate. The data types that Bruker exports include ser and fid files; however, they are always accompanied by a method text file that contains all the necessary information for the MRSinMRS table. The nomenclature in the method files remains unchanged across versions (here tested PV6.0.1, PV 360 V1.1, PV 360 V3.3); therefore we chose to read this file type for our application. Figure 5. Exported output from the REMY standalone application using a Siemens .twix MRS dataset. The first the table regarding data acquisition and hardware are populated, while data processing and quality need to be manually inputted by the researchers.
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By automatically populating a standard table suggested by a consensus paper, sourced from a single MRS data file, the process facilitates straightforward study replication and streamlined method evaluation. Furthermore, the tool generates a methods section, simplifying the reporting process for researchers, which can help ensure the validity of the study setup and the interpretability of the results. The alternative requires a complete manual search for those parameters, and exporting and populating the table justified in the consensus paper.15 While our REMY tool populates the
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