A consensus protocol for functional connectivity analysis in the rat brain
2023
Grandjean, Joanes | Desrosiers-Gregoire, Gabriel | Anckaerts, Cynthia | Angeles-Valdez, Diego | Ayad, Fadi | Barrière, David, A | Blockx, Ines | Bortel, Aleksandra | Broadwater, Margaret | Cardoso, Beatriz, M | Célestine, Marina | Chavez-Negrete, Jorge, E | Choi, Sangcheon | Christiaen, Emma | Clavijo, Perrin | Colon-Perez, Luis | Cramer, Samuel | Daniele, Tolomeo | Dempsey, Elaine | Diao, Yujian | Doelemeyer, Arno | Dopfel, David | Dvořáková, Lenka | Falfán-Melgoza, Claudia | Fernandes, Francisca, F | Fowler, Caitlin, F | Fuentes-Ibañez, Antonio | Garin, Clément, M | Gelderman, Eveline | Golden, Carla, E M | Guo, Chao, C G | Henckens, Marloes, J a G | Hennessy, Lauren, A | Herman, Peter | Hofwijks, Nita | Horien, Corey | Ionescu, Tudor, M | Jones, Jolyon | Kaesser, Johannes | Kim, Eugene | Lambers, Henriette | Lazari, Alberto | Lee, Sung-Ho | Lillywhite, Amanda | Liu, Yikang | Liu, Yanyan, Y | López -Castro, Alejandra | López-Gil, Xavier | Ma, Zilu | Macnicol, Eilidh | Madularu, Dan | Mandino, Francesca | Marciano, Sabina | Mcauslan, Matthew, J | Mccunn, Patrick | Mcintosh, Alison | Meng, Xianzong | Meyer-Baese, Lisa | Missault, Stephan | Moro, Federico | Naessens, Daphne, M P | Nava-Gomez, Laura, J | Nonaka, Hiroi | Ortiz, Juan, J | Paasonen, Jaakko | Peeters, Lore, M | Pereira, Mickaël | Perez, Pablo, D | Pompilus, Marjory | Prior, Malcolm | Rakhmatullin, Rustam | Reimann, Henning, M | Reinwald, Jonathan | del Rio, Rodrigo, Triana | Rivera-Olvera, Alejandro | Ruiz-Pérez, Daniel | Russo, Gabriele | Rutten, Tobias, J | Ryoke, Rie | Sack, Markus | Salvan, Piergiorgio | Sanganahalli, Basavaraju, G | Schroeter, Aileen | Seewoo, Bhedita, J | Selingue, Erwan | Seuwen, Aline | Shi, Bowen | Sirmpilatze, Nikoloz | Smith, Joanna, a B | Smith, Corrie | Sobczak, Filip | Stenroos, Petteri, J | Straathof, Milou | Strobelt, Sandra | Sumiyoshi, Akira | Takahashi, Kengo | Torres-García, Maria, E | Tudela, Raul | van den Berg, Monica | van der Marel, Kajo | van Hout, Aran, T B | Vertullo, Roberta | Vidal, Benjamin | Vrooman, Roël, M | Wang, Victora, X | Wank, Isabel | Watson, David, J G | Yin, Ting | Zhang, Yongzhi | Zurbruegg, Stefan | Achard, Sophie | Alcauter, Sarael | Auer, Dorothee, P | Barbier, Emmanuel, L | Baudewig, Jürgen | Beckmann, Christian, F | Beckmann, Nicolau | Becq, Guillaume, Jean-Paul Claude | Blezer, Erwin, L A | Bolbos, Radu | Boretius, Susann | Bouvard, Sandrine | Budinger, Eike | Buxbaum, Joseph, D | Cash, Diana | Chapman, Victoria | Chuang, Kai-Hsiang | Ciobanu, Luisa | Coolen, Bram, F | Dalley, Jeffrey, W | Dhenain, Marc | Dijkhuizen, Rick, M | Esteban, Oscar | Faber, Cornelius | Febo, Marcelo | Feindel, Kirk, W | Forloni, Gianluigi | Fouquet, Jérémie | Garza-Villarreal, Eduardo, A | Gass, Natalia | Glennon, Jeffrey, C | Gozzi, Alessandro | Gröhn, Olli | Harkin, Andrew | Heerschap, Arend | Helluy, Xavier | Herfert, Kristina | Heuser, Arnd | Homberg, Judith, R | Houwing, Danielle, J | Hyder, Fahmeed | Ielacqua, Giovanna, Diletta | Jelescu, Ileana, O | Johansen-Berg, Heidi | Kaneko, Gen | Kawashima, Ryuta | Keilholz, Shella, D | Keliris, Georgios, A | Kelly, Clare | Kerskens, Christian | Khokhar, Jibran, Y | Kind, Peter, C | Langlois, Jean-Baptiste | Lerch, Jason, P | López-Hidalgo, Monica, A | Manahan-Vaughan, Denise | Marchand, Fabien | Mars, Rogier, B | Marsella, Gerardo | Micotti, Edoardo | Muñoz-Moreno, Emma | Near, Jamie | Niendorf, Thoralf | Otte, Willem, M | Pais-Roldán, Patricia | Pan, Wen-Ju | Prado-Alcalá, Roberto, A | Quirarte, Gina, L | Rodger, Jennifer | Rosenow, Tim | Sampaio-Baptista, Cassandra | Sartorius, Alexander | Sawiak, Stephen, J | Scheenen, Tom, W J | Shemesh, Noam | Shih, Yen-Yu Ian | Shmuel, Amir | Soria, Guadalupe | Stoop, Ron | Thompson, Garth, J | Till, Sally, M | Todd, Nick | van der Linden, Annemie | van der Toorn, Annette | van Tilborg, Geralda, a F | Vanhove, Christian | Veltien, Andor | Verhoye, Marleen | Wachsmuth, Lydia | Weber-Fahr, Wolfgang | Wenk, Patricia | Yu, Xin | Zerbi, Valerio | Zhang, Nanyin | Zhang, Baogui, B | Zimmer, Luc | Devenyi, Gabriel, A | Chakravarty, M. Mallar | Hess, Andreas | Radboud University Medical Center [Nijmegen] (RadboudUMC) | Douglas Mental Health University Institute [Montréal] ; McGill University = Université McGill [Montréal, Canada] | University of Antwerp (UA) | Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM) | McGill University = Université McGill [Montréal, Canada] | Physiologie de la reproduction et des comportements [Nouzilly] (PRC) ; Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | University of North Carolina [Chapel Hill] (UNC) ; University of North Carolina System (UNC) | Champalimaud Centre for the Unknown [Lisbon] | Molecular Imaging Research Center [Fontenay-aux-Roses] (MIRCEN) ; Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie François JACOB (JACOB) ; Direction de Recherche Fondamentale (CEA) (DRF (CEA)) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA) | Max Planck Institute for Biological Cybernetics ; Max-Planck-Gesellschaft | IBiTech-bioMMeda ; Universiteit Gent = Ghent University = Université de Gand (UGENT) | Emory University [Atlanta, GA] | University of North Texas Health Science Center [Fort Worth] | Pennsylvania State University (Penn State) ; Penn State System | University College of London [London] (UCL) | Trinity College Dublin | Ecole Polytechnique Fédérale de Lausanne (EPFL) | Novartis Institutes for BioMedical Research (NIBR) | University of Eastern Finland | Central Institute of Mental Health [Mannheim] ; University Hospital Mannheim | Universitätsmedizin Mannheim | Radboud University [Nijmegen] | Icahn School of Medicine at Mount Sinai [New York] (MSSM) | The University of Western Australia (UWA) | Yale School of Medicine [New Haven, Connecticut] (YSM) | Eberhard Karls Universität Tübingen = University of Tübingen | University of Cambridge [UK] (CAM) | Friedrich-Alexander Universität Erlangen-Nürnberg = University of Erlangen-Nuremberg (FAU) | King‘s College London | University Hospital Münster - Universitaetsklinikum Muenster [Germany] (UKM) | John Radcliffe Hospital [Oxford University Hospital] | University of Nottingham, UK (UON) | Chinese Academy of Sciences [Beijing] (CAS) | Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) ; Universitat de Barcelona (UB) | Northeastern University [Boston] | Yale University [New Haven] | Universitätsklinikum Tübingen - University Hospital of Tübingen ; Eberhard Karls Universität Tübingen = University of Tübingen | University of Western Ontario (UWO) | Georgia Institute of Technology [Atlanta] | IRCCS Istituto Nazionale dei Tumori [Milano] | University of Amsterdam [Amsterdam] = Universiteit van Amsterdam (UvA) | Universidad Autónoma de Querétaro (UAQ) | University of Florida [Gainesville] (UF) | Université Claude Bernard Lyon 1 (UCBL) ; Université de Lyon | Max Delbrück Center for Molecular Medicine [Berlin] (MDC) ; Helmholtz-Gemeinschaft = Helmholtz Association | University of Heidelberg, Medical Faculty | Centre Hospitalier Universitaire Vaudois = Lausanne University Hospital [Lausanne] (CHUV) | Ruhr University Bochum = Ruhr-Universität Bochum (RUB) | Tohoku University [Sendai] | University hospital of Zurich [Zurich] | Service NEUROSPIN (NEUROSPIN) ; Université Paris-Saclay-Institut des Sciences du Vivant Frédéric JOLIOT (JOLIOT) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA) | ShanghaiTech University [Shanghai] | Georg-August-University of Göttingen = Georg-August-Universität Göttingen | The University of Edinburgh | [GIN] Grenoble Institut des Neurosciences (GIN) ; Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA) | University Medical Center [Utrecht] (UMCU) | National Institutes for Quantum and Radiological Science and Technology (QST) | Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) | Brigham and Women's Hospital [Boston] | Modèles statistiques bayésiens et des valeurs extrêmes pour données structurées et de grande dimension (STATIFY) ; Centre Inria de l'Université Grenoble Alpes ; Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Kuntzmann (LJK) ; Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP) ; Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP) ; Université Grenoble Alpes (UGA) | German Primate Center - Deutsches Primatenzentrum - Leibniz Insitute for Primate Research [Göttingen] (GPC - DPZ) ; Leibniz Gemeinschaft | GIPSA Pôle Géométrie, Apprentissage, Information et Algorithmes (GIPSA-GAIA) ; Grenoble Images Parole Signal Automatique (GIPSA-lab) ; Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP) ; Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP) ; Université Grenoble Alpes (UGA) | GIPSA-Services (GIPSA-Services) ; Grenoble Images Parole Signal Automatique (GIPSA-lab) ; Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP) ; Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP) ; Université Grenoble Alpes (UGA) | Centre d'Etude et de Recherche Multimodal Et Pluridisciplinaire en imagerie du vivant (CERMEP - imagerie du vivant) ; Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E)-Université Claude Bernard Lyon 1 (UCBL) ; Université de Lyon-Université de Lyon-Centre Hospitalier Universitaire [CHU Grenoble] (CHUGA)-Hospices Civils de Lyon (HCL)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA) | Radiopharmaceutical and Neurochemical Biomarkers (CRNL-BIORAN) ; Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL) ; Université Claude Bernard Lyon 1 (UCBL) ; Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL) ; Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS) | Leibniz Institute for Neurobiology [Magdeburg] (LIN) | The University of Queensland (UQ [All campuses : Brisbane, Dutton Park Gatton, Herston, St Lucia and other locations]) | Laboratoire des Maladies Neurodégénératives - UMR 9199 (LMN) ; Molecular Imaging Research Center [Fontenay-aux-Roses] (MIRCEN) ; Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie François JACOB (JACOB) ; Direction de Recherche Fondamentale (CEA) (DRF (CEA)) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie François JACOB (JACOB) ; Direction de Recherche Fondamentale (CEA) (DRF (CEA)) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS) | Université de Lausanne = University of Lausanne (UNIL) | Westfälische Wilhelms-Universität Münster = University of Münster (WWU) | Istituto di Ricerche Farmacologiche "Mario Negri" = Mario Negri Institute for Pharmacological Research (IRCCS) | University College Dublin [Dublin] (UCD) | Italian Institute of Technology = Istituto Italiano di Tecnologia (IIT) | University of Houston-Victoria | Institute for Stem Cell Biology and Regenerative Medicine [Bengaluru] | University of Toronto | Neuro-Dol (Neuro-Dol) ; Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA) | Sunnybrook Research Institute [Toronto] (SRI) ; Sunnybrook Health Sciences Centre [Toronto] (Sunnybrook) | University of Glasgow | Universität Duisburg-Essen = University of Duisburg-Essen [Essen] | Universitat de Barcelona (UB) | Universiteit Gent = Ghent University = Université de Gand (UGENT) | Massachusetts General Hospital [Boston] | Harvard Medical School [Boston] (HMS) | Hospices Civils de Lyon (HCL) | ANR-11-INBS-0006,FLI,France Life Imaging(2011)
International audience
Show more [+] Less [-]English. Task-free functional connectivity in animal models provides an experimental framework to examine connectivity phenomena under controlled conditions and allows for comparisons with data modalities collected under invasive or terminal procedures. Currently, animal acquisitions are performed with varying protocols and analyses that hamper result comparison and integration. Here we introduce StandardRat, a consensus rat functional magnetic resonance imaging acquisition protocol tested across 20 centers. To develop this protocol with optimized acquisition and processing parameters, we initially aggregated 65 functional imaging datasets acquired from rats across 46 centers. We developed a reproducible pipeline for analyzing rat data acquired with diverse protocols and determined experimental and processing parameters associated with the robust detection of functional connectivity across centers. We show that the standardized protocol enhances biologically plausible functional connectivity patterns relative to previous acquisitions. The protocol and processing pipeline described here is openly shared with the neuroimaging community to promote interoperability and cooperation toward tackling the most important challenges in neuroscience.
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