. 2025 Aug 4;8(1):1149.

doi: 10.1038/s42003-025-08412-1.

fNIRS reproducibility varies with data quality, analysis pipelines, and researcher experience

Meryem A Yücel^#^{1

2}, Robert Luke^#^{3

4}, Rickson C Mesquita^#^{5

6}, Alexander von Lühmann^#^{7

8}, David M A Mehler^{9

10

11}, Michael Lührs¹², Jessica Gemignani^{13

14}, Androu Abdalmalak^{15

16}, Franziska Albrecht^{17

18}, Iara de Almeida Ivo¹², Christina Artemenko¹⁹, Kira Ashton²⁰, Paweł Augustynowicz²¹, Aahana Bajracharya²², Elise Bannier^{23

24}, Beatrix Barth^{25

26

27}, Laurie Bayet²⁰, Jacqueline Behrendt^{28

29}, Hadi Borj Khani³⁰, Lenaic Borot³¹, Jordan A Borrell^{32

33}, Sabrina Brigadoi¹³, Kolby Brink³², Chiara Bulgarelli³⁴, Emmanuel Caruyer²⁴, Hsin-Chin Chen³⁵, Christopher Copeland³², Isabelle Corouge²⁴, Simone Cutini^{13

14}, Renata Di Lorenzo^{36

37}, Thomas Dresler^{25

26

27}, Adam T Eggebrecht²², Ann-Christine Ehlis^{25

26

27}, Sinem B Erdoğan³⁸, Danielle Evenblij¹², Talukdar Raian Ferdous³⁹, Victoria Fracalossi²⁰, Erika Franzén^{17

18}, Anne Gallagher⁴⁰, Christian Gerloff^{41

42}, Judit Gervain^{13

14}, Noy Goldhamer⁴³, Louisa K Gossé³⁴, Ségolène M R Guérin^{44

45}, Edgar Guevara⁴⁶, S M Hadi Hosseini⁴⁷, Hamish Innes-Brown^{48

49}, Isabell Int-Veen²⁵, Sagi Jaffe-Dax⁵⁰, Nolwenn Jégou²⁴, Hiroshi Kawaguchi⁵¹, Caroline Kelsey^{36

37}, Michaela Kent⁵², Roman Kessler⁵³, Nadeen Kherbawy⁵⁰, Franziska Klein^{9

54

55}, Nofar Kochavi⁵⁰, Matthew Kolisnyk⁵⁶, Yogev Koren⁵⁷, Agnes Kroczek²⁵, Alexander Kvist¹⁷, Chen-Hao Paul Lin^{22

58}, Andreas Löw⁵⁹, Siying Luan⁶⁰, Darren Mao⁶¹, Giovani G Martins⁶², Eike Middell^{28

29}, Samuel Montero-Hernandez^{63

64}, Murat Can Mutlu⁶⁵, Sergio L Novi¹⁶, Natacha Paquette⁴⁰, Ishara Paranawithana⁶¹, Yisrael Parmet⁶⁶, Jonathan E Peelle⁶⁷, Ke Peng⁶⁸, Tommy Peng⁶¹, João Pereira^{12

69}, Paola Pinti³⁴, Luca Pollonini⁷⁰, Ali Rahimpour Jounghani^{47

71}, Vanessa Reindl^{41

72}, Wiebke Ringels⁹, Betti Schopp²⁵, Alina Schulte^{48

73}, Martin Schulte-Rüther^{74

75}, Ari Segel²², Tirdad Seifi Ala^{48

49}, Maureen J Shader⁷⁶, Hadas Shavit⁵⁰, Arefeh Sherafati^{22

77}, Mojtaba Soltanlou^{78

79}, Bettina Sorger¹², Emma Speh²², Kevin D Stubbs^{15

80}, Katharina Stute⁸¹, Eileen F Sullivan³⁶, Sungho Tak^{82

83}, Zeus Tipado⁸⁴, Julie Tremblay⁴⁰, Homa Vahidi⁵², Maaike Van Eeckhoutte^{49

85}, Phetsamone Vannasing⁴⁰, Gregoire Vergotte⁸⁶, Marion A Vincent⁴⁵, Eileen Weiss⁸⁷, Dalin Yang²², Gülnaz Yükselen³⁸, Dariusz Zapała²¹, Vit Zemanek⁸⁸

Affiliations

¹ Boston University, Neurophotonics Center, Boston, MA, USA. mayucel@bu.edu.
² Department of Biomedical Engineering, College of Engineering, Boston University, Boston, MA, USA. mayucel@bu.edu.
³ Department of Linguistics, Macquarie University, Sydney, NSW, Australia.
⁴ Australia Hearing Hub, Macquarie University Hearing, Sydney, NSW, Australia.
⁵ School of Computer Science, University of Birmingham, Birmingham, UK. r.c.mesquita@bham.ac.uk.
⁶ Institute of Physics, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil. r.c.mesquita@bham.ac.uk.
⁷ Intelligent Biomedical Sensing (IBS) Lab, Machine Learning Department, TU Berlin, Berlin, Germany. vonluehmann@tu-berlin.de.
⁸ BIFOLD - Berlin Institute for Foundations of Learning and Data, Berlin, Germany. vonluehmann@tu-berlin.de.
⁹ Applied Computational Neuroscience (ACN) lab, Department for Psychiatry, Psychotherapy and Psychosomatics, Medical School, RWTH Aachen University, Aachen, Germany.
¹⁰ Institute of Translational Psychiatry, Medical Faculty, University of Münster, Münster, Germany.
¹¹ School of Psychology, Cardiff University Brain Research Imaging Center (CUBRIC), Cardiff University, Cardiff, UK.
¹² Department of Cognitive Neuroscience, Maastricht University, Maastricht, The Netherlands.
¹³ Department of Developmental Psychology and Socialization, Università degli Studi di Padova, Padua, Italy.
¹⁴ Padova Neuroscience Center, Padua, Italy.
¹⁵ Brain and Mind Institute, Western University, London, ON, Canada.
¹⁶ Department of Physiology and Pharmacology, Western University, London, ON, Canada.
¹⁷ Division of Physiotherapy, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden.
¹⁸ Karolinska University Hospital, Women's Health and Allied Health Professionals Theme, Medical Unit Occupational Therapy, Stockholm, Sweden.
¹⁹ Department of Psychology, University of Tübingen, Tübingen, Germany.
²⁰ Department of Neuroscience, American University, Washington, WA, USA.
²¹ Department of Experimental Psychology, The John Paul II Catholic University of Lublin, Lublin, Poland.
²² Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, WA, USA.
²³ CHU Rennes, Radiology Department, Rennes, France.
²⁴ Univ Rennes, Inria, CNRS, Inserm, IRISA UMR 6074, Empenn, Rennes, France.
²⁵ Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, University of Tübingen, Tübingen, Germany.
²⁶ LEAD Graduate School & Research Network, University of Tübingen, Tübingen, Germany.
²⁷ German Center for Mental Health (DZPG), partner site, Tübingen, Germany.
²⁸ Intelligent Biomedical Sensing (IBS) Lab, Machine Learning Department, TU Berlin, Berlin, Germany.
²⁹ BIFOLD - Berlin Institute for Foundations of Learning and Data, Berlin, Germany.
³⁰ BEARLabs, Faculty 1, University of Applied Sciences (HTW) Berlin, Berlin, Germany.
³¹ Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, England.
³² Department of Biomechanics, University of Nebraska at Omaha, Omaha, NE, USA.
³³ Department of Occupational Therapy Education, University of Kansas Medical Center, Kansas City, KS, USA.
³⁴ Centre for Brain and Cognitive Development, Birkbeck, University of London, London, UK.
³⁵ Department of Psychology, National Chung Cheng University, Minhsiung, Chiayi, Taiwan.
³⁶ Division of Developmental Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
³⁷ Harvard Medical School, Boston, MA, USA.
³⁸ Faculty of Engineering and Natural Sciences, Department of Biomedical Engineering, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey.
³⁹ Department of Biomedical Engineering, University of Houston, Houston, TX, USA.
⁴⁰ Department of Psychology, University of Montreal, Montreal, QC, Canada.
⁴¹ Department of Child and Adolescent Psychiatry, RWTH Aachen University, Aachen, Germany.
⁴² JARA-Brain Institute II, Molecular Neuroscience and Neuroimaging, RWTH Aachen & Research Centre Juelich, Aachen, Germany.
⁴³ The Translational Neurorehabilitation Lab at Adi Negev Nahalat Eran, Ofakim, Israel.
⁴⁴ Institute of Neuroscience, Université Catholique de Louvain, Brussels, Belgium.
⁴⁵ Sciences Cognitives et Sciences Affectives, University of Lille, CNRS, Lille, France.
⁴⁶ CIACYT, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico.
⁴⁷ Department of Psychiatry and Behavioral Sciences, Computational Brain Research and Intervention (C-BRAIN) Lab, Stanford University, Stanford, CA, USA.
⁴⁸ Eriksholm Research Centre, Snekkersten, Denmark.
⁴⁹ Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.
⁵⁰ School of Psychological Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
⁵¹ Human Informatics and Interaction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
⁵² Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.
⁵³ Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.
⁵⁴ Neurocognition and functional Neurorehabilitation Group, Department of Psychology, University of Oldenburg, Oldenburg, Germany.
⁵⁵ Biomedical Devices and Systems Group, R&D Division Health, OFFIS Institute for Information Technology, Oldenburg, Germany.
⁵⁶ Department of Psychology, Western University, London, ON, Canada.
⁵⁷ Department of Physical Therapy, Ben-Gurion University, Beersheba, Israel.
⁵⁸ Department of Physics, Washington University in St. Louis, St. Louis, MO, USA.
⁵⁹ Experimental Psychology Unit, Helmut Schmidt University/University of the Federal Armed Forces Hamburg, Hamburg, Germany.
⁶⁰ Health and Rehabilitation Sciences Program, Faculty of Health Science, Western University, London, ON, Canada.
⁶¹ Human Hearing, The Bionics Institute, East Melbourne, VIC, Australia.
⁶² Institute of Physics, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
⁶³ Boston University, Neurophotonics Center, Boston, MA, USA.
⁶⁴ Department of Biomedical Engineering, College of Engineering, Boston University, Boston, MA, USA.
⁶⁵ Institute of Biology, Otto von Guericke University, Magdeburg, Germany.
⁶⁶ Industrial engineering and management, Ben-Gurion university, Beersheba, Israel.
⁶⁷ Department of Communication Sciences and Disorders and Department of Psychology, Northeastern University, Boston, MA, USA.
⁶⁸ Department of Electrical and Computer Engineering, Price Faculty of Engineering, University of Manitoba, Winnipeg, MB, Canada.
⁶⁹ Coimbra Institute for Biomedical Imaging and Translational Research, Institute for Nuclear Sciences Applied to Health - University of Coimbra, Coimbra, Portugal.
⁷⁰ Department of Engineering Technology, University of Houston, Houston, TX, USA.
⁷¹ Department of Psychology, University of California, Merced, Merced, CA, USA.
⁷² Psychology, School of Social Sciences, Nanyang Technological University, Singapore, Republic of Singapore.
⁷³ Department of Experimental Otology of the Clinics of Otolaryngology, Hannover Medical School, Hannover, Germany.
⁷⁴ Department of Child and Adolescent Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany.
⁷⁵ Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital Heidelberg, Heidelberg, Germany.
⁷⁶ Department of Speech, Language, and Hearing Sciences, Purdue University, West Lafayette, IN, USA.
⁷⁷ Department of Neurology, University of California, San Francisco, CA, USA.
⁷⁸ School of Psychology, University of Surrey, Guildford, UK.
⁷⁹ Department of Childhood Education, Faculty of Education, University of Johannesburg, Johannesburg, South Africa.
⁸⁰ BrainsCAN, Western University, London, ON, Canada.
⁸¹ Chemnitz University of Technology, Faculty of Behavioural and Social Sciences, Department of Human Movement Science and Health, Chemnitz, Germany.
⁸² Center for Bio-Imaging and Translational Research, Korea Basic Science Institute, Cheongju, Republic of Korea.
⁸³ Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea.
⁸⁴ Department of Psychopharmacology, Maastricht University, Maastricht, The Netherlands.
⁸⁵ Copenhagen Hearing and Balance Centre, Rigshospitalet, Copenhagen, Denmark.
⁸⁶ EuroMov Digital Health in Motion, Univ Montpellier, IMT Mines Ales, Montpellier, France.
⁸⁷ Department of Clinical Neuropsychology, University Hospital RWTH Aachen, Aachen, Germany.
⁸⁸ Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands.

^# Contributed equally.

PMID: 40760004
PMCID: PMC12322209
DOI: 10.1038/s42003-025-08412-1

fNIRS reproducibility varies with data quality, analysis pipelines, and researcher experience

Meryem A Yücel et al. Commun Biol. 2025.

. 2025 Aug 4;8(1):1149.

doi: 10.1038/s42003-025-08412-1.

Authors

Affiliations

¹ Boston University, Neurophotonics Center, Boston, MA, USA. mayucel@bu.edu.
² Department of Biomedical Engineering, College of Engineering, Boston University, Boston, MA, USA. mayucel@bu.edu.
³ Department of Linguistics, Macquarie University, Sydney, NSW, Australia.
⁴ Australia Hearing Hub, Macquarie University Hearing, Sydney, NSW, Australia.
⁵ School of Computer Science, University of Birmingham, Birmingham, UK. r.c.mesquita@bham.ac.uk.
⁶ Institute of Physics, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil. r.c.mesquita@bham.ac.uk.
⁷ Intelligent Biomedical Sensing (IBS) Lab, Machine Learning Department, TU Berlin, Berlin, Germany. vonluehmann@tu-berlin.de.
⁸ BIFOLD - Berlin Institute for Foundations of Learning and Data, Berlin, Germany. vonluehmann@tu-berlin.de.
⁹ Applied Computational Neuroscience (ACN) lab, Department for Psychiatry, Psychotherapy and Psychosomatics, Medical School, RWTH Aachen University, Aachen, Germany.
¹⁰ Institute of Translational Psychiatry, Medical Faculty, University of Münster, Münster, Germany.
¹¹ School of Psychology, Cardiff University Brain Research Imaging Center (CUBRIC), Cardiff University, Cardiff, UK.
¹² Department of Cognitive Neuroscience, Maastricht University, Maastricht, The Netherlands.
¹³ Department of Developmental Psychology and Socialization, Università degli Studi di Padova, Padua, Italy.
¹⁴ Padova Neuroscience Center, Padua, Italy.
¹⁵ Brain and Mind Institute, Western University, London, ON, Canada.
¹⁶ Department of Physiology and Pharmacology, Western University, London, ON, Canada.
¹⁷ Division of Physiotherapy, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden.
¹⁸ Karolinska University Hospital, Women's Health and Allied Health Professionals Theme, Medical Unit Occupational Therapy, Stockholm, Sweden.
¹⁹ Department of Psychology, University of Tübingen, Tübingen, Germany.
²⁰ Department of Neuroscience, American University, Washington, WA, USA.
²¹ Department of Experimental Psychology, The John Paul II Catholic University of Lublin, Lublin, Poland.
²² Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, WA, USA.
²³ CHU Rennes, Radiology Department, Rennes, France.
²⁴ Univ Rennes, Inria, CNRS, Inserm, IRISA UMR 6074, Empenn, Rennes, France.
²⁵ Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, University of Tübingen, Tübingen, Germany.
²⁶ LEAD Graduate School & Research Network, University of Tübingen, Tübingen, Germany.
²⁷ German Center for Mental Health (DZPG), partner site, Tübingen, Germany.
²⁸ Intelligent Biomedical Sensing (IBS) Lab, Machine Learning Department, TU Berlin, Berlin, Germany.
²⁹ BIFOLD - Berlin Institute for Foundations of Learning and Data, Berlin, Germany.
³⁰ BEARLabs, Faculty 1, University of Applied Sciences (HTW) Berlin, Berlin, Germany.
³¹ Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, England.
³² Department of Biomechanics, University of Nebraska at Omaha, Omaha, NE, USA.
³³ Department of Occupational Therapy Education, University of Kansas Medical Center, Kansas City, KS, USA.
³⁴ Centre for Brain and Cognitive Development, Birkbeck, University of London, London, UK.
³⁵ Department of Psychology, National Chung Cheng University, Minhsiung, Chiayi, Taiwan.
³⁶ Division of Developmental Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
³⁷ Harvard Medical School, Boston, MA, USA.
³⁸ Faculty of Engineering and Natural Sciences, Department of Biomedical Engineering, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey.
³⁹ Department of Biomedical Engineering, University of Houston, Houston, TX, USA.
⁴⁰ Department of Psychology, University of Montreal, Montreal, QC, Canada.
⁴¹ Department of Child and Adolescent Psychiatry, RWTH Aachen University, Aachen, Germany.
⁴² JARA-Brain Institute II, Molecular Neuroscience and Neuroimaging, RWTH Aachen & Research Centre Juelich, Aachen, Germany.
⁴³ The Translational Neurorehabilitation Lab at Adi Negev Nahalat Eran, Ofakim, Israel.
⁴⁴ Institute of Neuroscience, Université Catholique de Louvain, Brussels, Belgium.
⁴⁵ Sciences Cognitives et Sciences Affectives, University of Lille, CNRS, Lille, France.
⁴⁶ CIACYT, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico.
⁴⁷ Department of Psychiatry and Behavioral Sciences, Computational Brain Research and Intervention (C-BRAIN) Lab, Stanford University, Stanford, CA, USA.
⁴⁸ Eriksholm Research Centre, Snekkersten, Denmark.
⁴⁹ Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.
⁵⁰ School of Psychological Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
⁵¹ Human Informatics and Interaction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
⁵² Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.
⁵³ Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.
⁵⁴ Neurocognition and functional Neurorehabilitation Group, Department of Psychology, University of Oldenburg, Oldenburg, Germany.
⁵⁵ Biomedical Devices and Systems Group, R&D Division Health, OFFIS Institute for Information Technology, Oldenburg, Germany.
⁵⁶ Department of Psychology, Western University, London, ON, Canada.
⁵⁷ Department of Physical Therapy, Ben-Gurion University, Beersheba, Israel.
⁵⁸ Department of Physics, Washington University in St. Louis, St. Louis, MO, USA.
⁵⁹ Experimental Psychology Unit, Helmut Schmidt University/University of the Federal Armed Forces Hamburg, Hamburg, Germany.
⁶⁰ Health and Rehabilitation Sciences Program, Faculty of Health Science, Western University, London, ON, Canada.
⁶¹ Human Hearing, The Bionics Institute, East Melbourne, VIC, Australia.
⁶² Institute of Physics, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
⁶³ Boston University, Neurophotonics Center, Boston, MA, USA.
⁶⁴ Department of Biomedical Engineering, College of Engineering, Boston University, Boston, MA, USA.
⁶⁵ Institute of Biology, Otto von Guericke University, Magdeburg, Germany.
⁶⁶ Industrial engineering and management, Ben-Gurion university, Beersheba, Israel.
⁶⁷ Department of Communication Sciences and Disorders and Department of Psychology, Northeastern University, Boston, MA, USA.
⁶⁸ Department of Electrical and Computer Engineering, Price Faculty of Engineering, University of Manitoba, Winnipeg, MB, Canada.
⁶⁹ Coimbra Institute for Biomedical Imaging and Translational Research, Institute for Nuclear Sciences Applied to Health - University of Coimbra, Coimbra, Portugal.
⁷⁰ Department of Engineering Technology, University of Houston, Houston, TX, USA.
⁷¹ Department of Psychology, University of California, Merced, Merced, CA, USA.
⁷² Psychology, School of Social Sciences, Nanyang Technological University, Singapore, Republic of Singapore.
⁷³ Department of Experimental Otology of the Clinics of Otolaryngology, Hannover Medical School, Hannover, Germany.
⁷⁴ Department of Child and Adolescent Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany.
⁷⁵ Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital Heidelberg, Heidelberg, Germany.
⁷⁶ Department of Speech, Language, and Hearing Sciences, Purdue University, West Lafayette, IN, USA.
⁷⁷ Department of Neurology, University of California, San Francisco, CA, USA.
⁷⁸ School of Psychology, University of Surrey, Guildford, UK.
⁷⁹ Department of Childhood Education, Faculty of Education, University of Johannesburg, Johannesburg, South Africa.
⁸⁰ BrainsCAN, Western University, London, ON, Canada.
⁸¹ Chemnitz University of Technology, Faculty of Behavioural and Social Sciences, Department of Human Movement Science and Health, Chemnitz, Germany.
⁸² Center for Bio-Imaging and Translational Research, Korea Basic Science Institute, Cheongju, Republic of Korea.
⁸³ Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea.
⁸⁴ Department of Psychopharmacology, Maastricht University, Maastricht, The Netherlands.
⁸⁵ Copenhagen Hearing and Balance Centre, Rigshospitalet, Copenhagen, Denmark.
⁸⁶ EuroMov Digital Health in Motion, Univ Montpellier, IMT Mines Ales, Montpellier, France.
⁸⁷ Department of Clinical Neuropsychology, University Hospital RWTH Aachen, Aachen, Germany.
⁸⁸ Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands.

^# Contributed equally.

PMID: 40760004
PMCID: PMC12322209
DOI: 10.1038/s42003-025-08412-1

Erratum in

Publisher Correction: fNIRS reproducibility varies with data quality, analysis pipelines, and researcher experience.
Yücel MA, Luke R, Mesquita RC, von Lühmann A, Mehler DMA, Lührs M, Gemignani J, Abdalmalak A, Albrecht F, de Almeida Ivo I, Artemenko C, Ashton K, Augustynowicz P, Bajracharya A, Bannier E, Barth B, Bayet L, Behrendt J, Khani HB, Borot L, Borrell JA, Brigadoi S, Brink K, Bulgarelli C, Caruyer E, Chen HC, Copeland C, Corouge I, Cutini S, Di Lorenzo R, Dresler T, Eggebrecht AT, Ehlis AC, Erdoğan SB, Evenblij D, Ferdous TR, Fracalossi V, Franzén E, Gallagher A, Gerloff C, Gervain J, Goldhamer N, Gossé LK, Guérin SMR, Guevara E, Hosseini SMH, Innes-Brown H, Int-Veen I, Jaffe-Dax S, Jégou N, Kawaguchi H, Kelsey C, Kent M, Kessler R, Kherbawy N, Klein F, Kochavi N, Kolisnyk M, Koren Y, Kroczek A, Kvist A, Lin CP, Löw A, Luan S, Mao D, Martins GG, Middell E, Montero-Hernandez S, Mutlu MC, Novi SL, Paquette N, Paranawithana I, Parmet Y, Peelle JE, Peng K, Peng T, Pereira J, Pinti P, Pollonini L, Jounghani AR, Reindl V, Ringels W, Schopp B, Schulte A, Schulte-Rüther M, Segel A, Ala TS, Shader MJ, Shavit H, Sherafati A, Soltanlou M, Sorger B, Speh E, Stubbs KD, Stute K, Sullivan EF, Tak S, Tipado Z, Tremblay J, Vahidi H, Van Eeckhoutte M, Vannasing P, Vergotte G, Vincent MA, Weiss E, Yang D… See abstract for full author list ➔ Yücel MA, et al. Commun Biol. 2025 Aug 21;8(1):1256. doi: 10.1038/s42003-025-08714-4. Commun Biol. 2025. PMID: 40841463 Free PMC article. No abstract available.

Abstract

As data analysis pipelines grow more complex in brain imaging research, understanding how methodological choices affect results is essential for ensuring reproducibility and transparency. This is especially relevant for functional Near-Infrared Spectroscopy (fNIRS), a rapidly growing technique for assessing brain function in naturalistic settings and across the lifespan, yet one that still lacks standardized analysis approaches. In the fNIRS Reproducibility Study Hub (FRESH) initiative, we asked 38 research teams worldwide to independently analyze the same two fNIRS datasets. Despite using different pipelines, nearly 80% of teams agreed on group-level results, particularly when hypotheses were strongly supported by literature. Teams with higher self-reported analysis confidence, which correlated with years of fNIRS experience, showed greater agreement. At the individual level, agreement was lower but improved with better data quality. The main sources of variability were related to how poor-quality data were handled, how responses were modeled, and how statistical analyses were conducted. These findings suggest that while flexible analytical tools are valuable, clearer methodological and reporting standards could greatly enhance reproducibility. By identifying key drivers of variability, this study highlights current challenges and offers direction for improving transparency and reliability in fNIRS research.

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Conflict of interest statement

Competing interests: The authors declare the following competing interests: D.Z. and P.A. are employees and shareholders in Cortivision sp. z o.o. (Lublin, Poland), a company that manufactures fNIRS systems. M.L. is employed by the research company Brain Innovation B.V., Maastricht, Netherlands. K.S. is employed by the (f)NIRS manufacturer Artinis Medical Systems B.V., Elst, The Netherlands. A.A. is employed by NIRx Medical Technologies, LLC. The remaining authors declare no competing interests.

Figures

**Fig. 1. Variability in hypothesis testing results across teams.**
A Proportion of teams supporting each group-level hypothesis, H, in Dataset I (see text for the description of each hypothesis). B Percentage of teams supporting each individual-level hypothesis in Dataset II, separated by subject, S. In both panels, bar segments indicate the fraction of teams that supported (‘YES,’ green), rejected (‘NO,’ blue), or did not test (‘Not Investigated,’ navy), and the numbers in each bar represent the percentage of each response. C Proportion of teams reporting a significant result among those that tested the hypothesis in Dataset I (n = 31 (H1, H2), n = 30 (H3), n = 35 (H4-H7)). D Proportion of teams reporting a significant result among those that tested the hypothesis in Dataset II (n = 30–34 (H1, depending on the subject), n = 28–33 (H2, depending on subject), n = 28–38 (H3), n = 27–32 (H4)). Each color represents a different participant. (FT finger tapping, PMC primary motor cortex, LIFG left inferior frontal gyrus, HG Herschl’s gyrus).

**Fig. 2. Overview of signal processing pipeline choices across teams.**
The teams’ pipeline choices for signal processing to extract the hemodynamic brain responses for subsequent statistical analysis are shown in a Sankey flow diagram with stages grouping choices by typical processing categories. All numbers are given in % rounded to two digits without decimal digits to improve readability. Multiple combined toolboxes in the analysis count individually toward each category (sum > 100%) in the pie chart. Processing stages: Pruning – method for identifying channels to drop from the analysis; (SCI) Scalp Coupling Index, (PSP) Peak Spectral Power, (SNR) Signal to Noise Ratio. Motion Artifacts – method for mitigating motion artifacts; (CBSI) Correlation Based Signal Improvement, (TDDR) Temporal Derivative Distribution Repair, (Spline SG) Spline interpolation with Savitzky-Golay filtering, (Mon. Interp.) Monotonous Interpolation. Resampling – resampling to a new sample rate for analysis. Filtering – temporal filtering. Physio. Preproc. – Other preprocessing *methods* for removal of physiological nuisance signals before HRF extraction. HRF Estimation – method for extraction/estimation of the hemodynamic brain response, GLM General Linear Model. Solvers/Modifiers – details for HRF estimation. (OLS) Ordinary Least Squares solution, (AR-IRLS) Autoregressive Iteratively Reweighted Least Squares. HRF Regressors – (only GLM) choice of regressors to model the hemodynamic response; (Consec. Gaussian) Consecutive Gaussians, (SPM) Statistical Parametric Mapping, (FIR) Finite Impulse Response. Other Regressors – (only GLM) choice of additional regressors to model physiology; (SC) Short Channels, (PCA of SC) First Principal Components of all Short Channels.

**Fig. 3. Reported statistical analysis steps for fNIRS data analysis pipelines.**
The teams’ pipeline choices to test the working hypotheses of this study are shown in a Sankey flow diagram with stages grouping choices by typical analysis categories based on n = 38 pipelines for each of the two datasets. Multiple combined toolboxes in analysis count individually to each category (sum > 100%) in the pie chart. Statistical stages: Stat. Method – Statistical method employed for hypothesis testing. (t-Test NN) t-Test without further specification of type. (Mixed Effects NN) Mixed Effects model without further specification of type. Signal Type – tests performed on brain responses measured via HbO, HbR, both, or other. All numbers are given in % rounded to two digits without decimal digits to improve readability. Signal Space – tests performed on responses from individual channels, in image space, or for regions of interest (ROI). Metric – tests performed on GLM beta weights, windowed signal amplitude, or other options. Test for Normality – no or if yes, which one; (Kolmog.-Smirn.) Kolmogorov–Smirnov Test. Significance Level – Threshold for statistical significance. Multiple Comparison Correction – none or three different approaches.

**Fig. 4. Reported use of toolbox default settings across analysis pipelines.**
UpSet plot showing the use of default parameters and settings in the groups’ analysis pipelines based on n = 38 pipelines for each of the two datasets. Rows display individual categories for which default settings could be chosen, and horizontal bar plots their cumulative frequency (e.g., groups chose default filter parameters in 47% of all reported analyses). The pie chart shows the fraction of groups that used default settings in 1, 2, 3, 4 and 5x categories (matching the color code of the intersection size bars, e.g. 2.9% used defaults for 5 categories). Connected black dots in columns display intersection (combination) of categories and vertical bar plots the frequency (intersection size) of these combinations. For example, three groups reported using default settings for the GLM method, artifact correction, and filter parameters combined, and four groups reported using the default settings only for the AR Model Order.

**Fig. 5. Distribution of pipeline choices by agreement with literature support.**
Radar Charts of the distribution of choices in the analysis pipelines based on their (dis-)agreement with expected hypotheses outcomes, grouped by different pipeline stages based on n = 38 pipelines. A Results for Hypotheses 1, 2, and 7 of Dataset I, which have been supported by prior literature and therefore have a high expectation of being confirmed. B Results for Hypothesis 3–6 of Dataset I, which are expected to be true but are only weakly supported by prior literature. C Results for all four hypotheses analyzed at the individual level in Dataset II. In all cases, radial axes numbers represent joint probabilities of pooled individual hypothesis outcomes for a chosen category among all users in percent.

**Fig. 6. Relationship between hypothesis testing outcomes and self-reported confidence.**
Panels A–C represent group-level hypotheses, while panels D–F illustrate individual-level hypotheses. Hypothesis testing results grouped by teams’ self-reported confidence in their analysis skills presented for group-level hypotheses (A) and individual-level hypotheses (D). Same results grouped by confidence in the reported outcomes presented for group-level hypotheses (B) and individual-level hypotheses (E). Sørensen-Dice similarity matrices illustrating the consistency of hypothesis outcomes across teams, organized according to self-reported confidence in their analysis skills presented for group-level hypotheses (C) and individual-level hypotheses (F). The colorbar represents the Sørensen-Dice coefficient values, ranging from 0.5 to 1. Please note that not all groups reported confidence; hence the number of groups in this plot is smaller than the total number of groups, which is 38.

**Fig. 7. Demographic profile of participating researchers.**
A total of 102 researchers, grouped in 38 teams, submitted reports for analysis. Plots show their A geographic affiliation, B years of experience in fNIRS, C highest education qualification, and D self-reported fields of study. (LA: Latin America, APAC: Asia and Pacific, ME: Middle East, HS: High School, UG: Undergraduate).

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References

1. Allen, C. & Mehler, D. M. A. Open science challenges, benefits and tips in early career and beyond. PLOS Biol.17, e3000246 (2019). - PMC - PubMed
1. Begley, C. G. & Ioannidis, J. P. A. Reproducibility in Science. Circ. Res.116, 116–126 (2015). - PubMed
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fNIRS reproducibility varies with data quality, analysis pipelines, and researcher experience

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fNIRS reproducibility varies with data quality, analysis pipelines, and researcher experience

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