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Journal Articles Nature Neuroscience Year : 2023

A consensus protocol for functional connectivity analysis in the rat brain

Joanes Grandjean (1) , Gabriel Desrosiers-Gregoire (2) , Cynthia Anckaerts (3) , Diego Angeles-Valdez (4) , Fadi Ayad (5) , David A Barrière (6) , Ines Blockx (3) , Aleksandra Bortel (5) , Margaret Broadwater (7) , Beatriz M Cardoso (8) , Marina Célestine (9) , Jorge E Chavez-Negrete (4) , Sangcheon Choi (10) , Emma Christiaen (11) , Perrin Clavijo (12) , Luis Colon-Perez (13) , Samuel Cramer (14) , Tolomeo Daniele (15) , Elaine Dempsey (16) , Yujian Diao (17) , Arno Doelemeyer (18) , David Dopfel (14) , Lenka Dvořáková (19) , Claudia Falfán-Melgoza (20) , Francisca F Fernandes (8) , Caitlin F Fowler (2, 5) , Antonio Fuentes-Ibañez (4) , Clément M Garin (9) , Eveline Gelderman (21) , Carla E M Golden (22) , Chao C G Guo (21) , Marloes J a G Henckens (21, 5) , Lauren A Hennessy (23) , Peter Herman (24) , Nita Hofwijks (21) , Corey Horien (24) , Tudor M Ionescu (25) , Jolyon Jones (26) , Johannes Kaesser (27) , Eugene Kim (28) , Henriette Lambers (29) , Alberto Lazari (30) , Sung-Ho Lee (7) , Amanda Lillywhite (31) , Yikang Liu (14) , Yanyan Y Liu (32) , Alejandra López -Castro (4) , Xavier López-Gil (33) , Zilu Ma (14) , Eilidh Macnicol (28) , Dan Madularu (5, 34) , Francesca Mandino (35) , Sabina Marciano (36) , Matthew J Mcauslan (16) , Patrick Mccunn (37) , Alison Mcintosh (15) , Xianzong Meng (21) , Lisa Meyer-Baese (38) , Stephan Missault (3) , Federico Moro (39) , Daphne M P Naessens (40) , Laura J Nava-Gomez (41) , Hiroi Nonaka (42) , Juan J Ortiz (4) , Jaakko Paasonen (19) , Lore M Peeters (3) , Mickaël Pereira (43) , Pablo D Perez (14) , Marjory Pompilus (42) , Malcolm Prior (31) , Rustam Rakhmatullin (16) , Henning M Reimann (44) , Jonathan Reinwald (45) , Rodrigo Triana del Rio (46) , Alejandro Rivera-Olvera (21) , Daniel Ruiz-Pérez (16) , Gabriele Russo (47) , Tobias J Rutten (21) , Rie Ryoke (48) , Markus Sack (20) , Piergiorgio Salvan (30) , Basavaraju G Sanganahalli (35) , Aileen Schroeter (49) , Bhedita J Seewoo (23) , Erwan Selingue (50) , Aline Seuwen (49) , Bowen Shi (51) , Nikoloz Sirmpilatze (52) , Joanna a B Smith (53) , Corrie Smith (12) , Filip Sobczak (10) , Petteri J Stenroos (54) , Milou Straathof (55) , Sandra Strobelt (27) , Akira Sumiyoshi (48, 56) , Kengo Takahashi (10, 36) , Maria E Torres-García (4) , Raul Tudela (57) , Monica van den Berg (3) , Kajo van der Marel (55) , Aran T B van Hout (21) , Roberta Vertullo (21) , Benjamin Vidal (43) , Roël M Vrooman (21) , Victora X Wang (22) , Isabel Wank (27) , David J G Watson (31) , Ting Yin (17) , Yongzhi Zhang (58) , Stefan Zurbruegg (18) , Sophie Achard (59) , Sarael Alcauter (4) , Dorothee P Auer (31) , Emmanuel L Barbier (54) , Jürgen Baudewig (60) , Christian F Beckmann (21, 30) , Nicolau Beckmann (18) , Guillaume J P C Becq (61, 62) , Erwin L A Blezer (55) , Radu Bolbos (63) , Susann Boretius (60, 52) , Sandrine Bouvard (43) , Eike Budinger (64) , Joseph D Buxbaum (22) , Diana Cash (28) , Victoria Chapman (31) , Kai-Hsiang Chuang (65) , Luisa Ciobanu (50) , Bram F Coolen (40) , Jeffrey W Dalley (26) , Marc Dhenain (66) , Rick M Dijkhuizen (55) , Oscar Esteban (46, 67) , Cornelius Faber (68) , Marcelo Febo (42) , Kirk W Feindel (23) , Gianluigi Forloni (69) , Jérémie Fouquet (2) , Eduardo A Garza-Villarreal (4) , Natalia Gass (20) , Jeffrey C Glennon (70) , Alessandro Gozzi (71) , Olli Gröhn (19) , Andrew Harkin (16) , Arend Heerschap (1) , Xavier Helluy (47) , Kristina Herfert (25) , Arnd Heuser (44) , Judith R Homberg (21) , Danielle J Houwing (21) , Fahmeed Hyder (35) , Giovanna Diletta Ielacqua (44) , Ileana O Jelescu (17) , Heidi Johansen-Berg (30) , Gen Kaneko (72) , Ryuta Kawashima (48) , Shella D Keilholz (12) , Georgios A Keliris (3) , Clare Kelly (16) , Christian Kerskens (16) , Jibran Y Khokhar (37) , Peter C Kind (53, 73) , Jean-Baptiste Langlois (63) , Jason P Lerch (30, 74) , Monica A López-Hidalgo (4) , Denise Manahan-Vaughan (47) , Fabien Marchand (75) , Rogier B Mars (21, 30) , Gerardo Marsella (69) , Edoardo Micotti (69) , Emma Muñoz-Moreno (33) , Jamie Near (2, 76) , Thoralf Niendorf (44) , Willem M Otte (55) , Patricia Pais-Roldán (10) , Wen-Ju Pan (12) , Roberto A Prado-Alcalá (4) , Gina L Quirarte (4) , Jennifer Rodger (23) , Tim Rosenow (23) , Cassandra Sampaio-Baptista (30, 77) , Alexander Sartorius (20) , Stephen J Sawiak (26) , Tom W J Scheenen (1, 78) , Noam Shemesh (8) , Yen-Yu Ian Shih (7) , Amir Shmuel (5) , Guadalupe Soria (79) , Ron Stoop (46) , Garth J Thompson (51) , Sally M Till (53) , Nick Todd (58) , Annemie van der Linden (3) , Annette van der Toorn (55) , Geralda a F van Tilborg (55) , Christian Vanhove (80) , Andor Veltien (1) , Marleen Verhoye (3) , Lydia Wachsmuth (68) , Wolfgang Weber-Fahr (20) , Patricia Wenk (64) , Xin Yu (81, 82) , Valerio Zerbi (17) , Nanyin Zhang (6) , Baogui B Zhang (32) , Luc Zimmer (43, 63, 83) , Gabriel A Devenyi (2, 5) , M. Mallar Chakravarty (2, 5) , Andreas Hess (27)
1 Radboud University Medical Center [Nijmegen]
2 Douglas Mental Health University Institute [Montréal]
3 UA - University of Antwerp
4 UNAM - Universidad Nacional Autónoma de México = National Autonomous University of Mexico
5 McGill University = Université McGill [Montréal, Canada]
6 PRC - Physiologie de la reproduction et des comportements [Nouzilly]
7 UNC - University of North Carolina [Chapel Hill]
8 Champalimaud Centre for the Unknown [Lisbon]
9 MIRCEN - Molecular Imaging Research Center [Fontenay-aux-Roses]
10 Max Planck Institute for Biological Cybernetics
11 IBiTech-bioMMeda
12 Emory University [Atlanta, GA]
13 University of North Texas Health Science Center [Fort Worth]
14 Penn State - Pennsylvania State University
15 UCL - University College of London [London]
16 Trinity College Dublin
17 EPFL - Ecole Polytechnique Fédérale de Lausanne
18 NIBR - Novartis Institutes for BioMedical Research
19 University of Eastern Finland
20 Central Institute of Mental Health [Mannheim]
21 Radboud University [Nijmegen]
22 MSSM - Icahn School of Medicine at Mount Sinai [New York]
23 UWA - The University of Western Australia
24 YSM - Yale School of Medicine [New Haven, Connecticut]
25 Eberhard Karls Universität Tübingen = University of Tübingen
26 CAM - University of Cambridge [UK]
27 FAU - Friedrich-Alexander Universität Erlangen-Nürnberg = University of Erlangen-Nuremberg
28 King‘s College London
29 UKM - University Hospital Münster - Universitaetsklinikum Muenster [Germany]
30 John Radcliffe Hospital [Oxford University Hospital]
31 UON - University of Nottingham, UK
32 CAS - Chinese Academy of Sciences [Beijing]
33 IDIBAPS - Institut d'Investigacions Biomèdiques August Pi i Sunyer
34 Northeastern University [Boston]
35 Yale University [New Haven]
36 Universitätsklinikum Tübingen - University Hospital of Tübingen
37 UWO - University of Western Ontario
38 Georgia Institute of Technology [Atlanta]
39 IRCCS Istituto Nazionale dei Tumori [Milano]
40 UvA - University of Amsterdam [Amsterdam] = Universiteit van Amsterdam
41 UAQ - Universidad Autónoma de Querétaro
42 UF - University of Florida [Gainesville]
43 UCBL - Université Claude Bernard Lyon 1
44 MDC - Max Delbrück Center for Molecular Medicine [Berlin]
45 University of Heidelberg, Medical Faculty
46 CHUV - Centre Hospitalier Universitaire Vaudois = Lausanne University Hospital [Lausanne]
47 RUB - Ruhr University Bochum = Ruhr-Universität Bochum
48 Tohoku University [Sendai]
49 University hospital of Zurich [Zurich]
50 NEUROSPIN - Service NEUROSPIN
51 ShanghaiTech University [Shanghai]
52 Georg-August-University = Georg-August-Universität Göttingen
53 Edin. - University of Edinburgh
54 GIN - [GIN] Grenoble Institut des Neurosciences
55 UMCU - University Medical Center [Utrecht]
56 QST - National Institutes for Quantum and Radiological Science and Technology
57 CIBER-BBN - Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina
58 Brigham and Women’s Hospital [Boston, MA]
59 STATIFY - Modèles statistiques bayésiens et des valeurs extrêmes pour données structurées et de grande dimension
60 GPC - DPZ - German Primate Center - Deutsches Primatenzentrum - Leibniz Insitute for Primate Research [Göttingen]
61 GIPSA-GAIA - GIPSA Pôle Géométrie, Apprentissage, Information et Algorithmes
62 GIPSA-Services - GIPSA-Services
63 CERMEP - imagerie du vivant - Centre d'Etude et de Recherche Multimodal Et Pluridisciplinaire en imagerie du vivant
64 LIN - Leibniz Institute for Neurobiology [Magdeburg]
65 UQ [All campuses : Brisbane, Dutton Park Gatton, Herston, St Lucia and other locations] - The University of Queensland
66 LMN - Laboratoire des Maladies Neurodégénératives - UMR 9199
67 UNIL - Université de Lausanne = University of Lausanne
68 WWU - Westfälische Wilhelms-Universität Münster = University of Münster
69 IRCCS - Istituto di Ricerche Farmacologiche "Mario Negri"
70 UCD - University College Dublin [Dublin]
71 IIT - Istituto Italiano di Tecnologia
72 University of Houston-Victoria
73 Institute for Stem Cell Biology and Regenerative Medicine [Bengaluru]
74 University of Toronto
75 Neuro-Dol - Neuro-Dol
76 SRI - Sunnybrook Research Institute [Toronto]
77 University of Glasgow
78 Universität Duisburg-Essen = University of Duisburg-Essen [Essen]
79 University of Barcelona
80 UGENT - Universiteit Gent = Ghent University
81 Massachusetts General Hospital [Boston]
82 HMS - Harvard Medical School [Boston]
83 HCL - Hospices Civils de Lyon
Emma Christiaen
  • Function : Author
Elaine Dempsey
Eveline Gelderman
Chao C G Guo
Lauren A Hennessy
Eugene Kim
Sung-Ho Lee
Amanda Lillywhite
Eilidh Macnicol
Francesca Mandino
Laura J Nava-Gomez
Mickaël Pereira
Basavaraju G Sanganahalli
Bhedita J Seewoo
Erwan Selingue
  • Function : Author
Bowen Shi
Monica van den Berg
Benjamin Vidal
Roël M Vrooman
Sandrine Bouvard
Diana Cash
Kai-Hsiang Chuang
Luisa Ciobanu
  • Function : Author
Alessandro Gozzi
Judith R Homberg
Fahmeed Hyder
Gen Kaneko
Shella D Keilholz
Georgios A Keliris
Clare Kelly
Fabien Marchand
Jennifer Rodger
Tim Rosenow
Stephen J Sawiak
Guadalupe Soria
Garth J Thompson
Christian Vanhove
Marleen Verhoye

Abstract

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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hal-04268925 , version 1 (04-11-2023)

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Joanes Grandjean, Gabriel Desrosiers-Gregoire, Cynthia Anckaerts, Diego Angeles-Valdez, Fadi Ayad, et al.. A consensus protocol for functional connectivity analysis in the rat brain. Nature Neuroscience, 2023, 26 (4), pp.673-681. ⟨10.1038/s41593-023-01286-8⟩. ⟨hal-04268925⟩
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