2023_Kalantari_AIDAqc/datacite.yml

# Metadata for DOI registration according to DataCite Metadata Schema 4.1.
# For detailed schema description see https://doi.org/10.5438/0014

## Required fields

# The main researchers involved. Include digital identifier (e.g., ORCID)
# if possible, including the prefix to indicate its type.
authors:
  -
    firstname: Aref
    lastname: Kalantari
    affiliation: 'University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Neurology, Cologne, Germany '
    id: 'ORCID:0000-0003-3050-0930'

  -
    firstname: Mehrab
    lastname: Shahbazi
    affiliation: 'Hamedan University of Technology, Faculty of Medical Engineering, Hamedan, Iran'
    id: ''
  -
    firstname: Marc
    lastname: Schneider
    affiliation: 'University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Neurology, Cologne, Germany'
    id: ''
  -
    firstname: Victor Vera
    lastname: Frazão
    affiliation: 'University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Neurology, Cologne, Germany'
    id: ''
  -
    firstname: Avnish
    lastname: Bhattrai
    affiliation: 'Center for Innovation in Brain Science, University of Arizona, Tucson, AZ, USA'
    id: ''
  -
    firstname: Lorenzo
    lastname: Carnevale
    affiliation: 'IRCCS INM Neuromed, Department of AngioCardioNeurology and Translational Medicine, Pozzilli, Italy'
    id: ''
  -
    firstname: Yujian
    lastname: Diao
    affiliation: 'Department of Radiology, Lausanne University Hospital (CHUV), Lausanne, Switzerland, and CIBM Center for Biomedical Imaging, Lausanne, Switzerland'
    id: ''
  -
    firstname: Bart A. A.
    lastname: Franx
    affiliation: 'Biomedical MR Imaging and Spectroscopy group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands'
    id: ''
  -
    firstname: Francesco
    lastname: Gammaraccio
    affiliation: 'Molecular Imaging Center, Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy'
    id: ''
  -
    firstname: Lisa-Marie
    lastname: Goncalves
    affiliation: 'Leibniz Institute for Neurobiology (LIN), Combinatorial Neuroimaging Core Facility (CNI), Magdeburg, Germany'
    id: ''
  -
    firstname: Susan
    lastname: Lee
    affiliation: 'Center for Behavioral Neuroscience, Neuroscience Institute, Advanced Translational Imaging Facility, Georgia State University, Atlanta, Georgia, USA'
    id: ''
  -
    firstname: Esther M.
    lastname: van Leeuwen
    affiliation: 'Biomedical MR Imaging and Spectroscopy group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands'
    id: ''
  -
    firstname: Annika
    lastname: Michalek
    affiliation: 'Leibniz Institute for Neurobiology (LIN), Combinatorial Neuroimaging Core Facility (CNI), Magdeburg, Germany'
    id: ''
  -
    firstname: Susanne
    lastname: Mueller
    affiliation: 'Department of Experimental Neurology and Center for Stroke Research Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany; Charité 3R | Replace, Reduce, Refine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; and NeuroCure Cluster of Excellence and Charité Core Facility 7T Experimental MRIs, Charité-Universitätsmedizin Berlin, Berlin, Germany'
    id: ''
  -
    firstname: Alejandro Rivera
    lastname: Olvera
    affiliation: 'Ikerbasque, Basque Foundation for Science, Bilbao, Spain'
    id: ''
  -
    firstname: Daniel
    lastname: Padro
    affiliation: 'Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain'
    id: ''
  -
    firstname: Adam C.
    lastname: Raikes
    affiliation: 'Center for Innovation in Brain Science, University of Arizona, Tucson, AZ, USA'
    id: ''
  -
    firstname: Mohamed Kotb
    lastname: Selim
    affiliation: 'Instituto de Neurociencias, CSIC/UMH, San Juan de Alicante, 03550 Alicante, Spain'
    id: ''
  -
    firstname: Annette
    lastname: van der Toorn
    affiliation: 'Biomedical MR Imaging and Spectroscopy group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands'
    id: ''
  -
    firstname: Federico
    lastname: Varriano
    affiliation: 'Laboratory of Surgical and Experimental Neuroanatomy, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, Barcelona, Spain'
    id: ''
  -
    firstname: Roël
    lastname: Vrooman
    affiliation: 'Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands'
    id: ''
  -
    firstname: Patricia
    lastname: Wenk
    affiliation: 'Leibniz Institute for Neurobiology (LIN), Combinatorial Neuroimaging Core Facility (CNI), Magdeburg, Germany'
    id: ''
  -
    firstname: H Elliott
    lastname: Albers
    affiliation: 'Center for Behavioral Neuroscience, Neuroscience Institute, Advanced Translational Imaging Facility, Georgia State University, Atlanta, Georgia, USA'
    id: ''
  -
    firstname: Philipp
    lastname: Boehm-Sturm
    affiliation: 'Department of Experimental Neurology and Center for Stroke Research Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany; Charité 3R | Replace, Reduce, Refine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; and NeuroCure Cluster of Excellence and Charité Core Facility 7T Experimental MRIs, Charité-Universitätsmedizin Berlin, Berlin, Germany'
    id: ''
  -
    firstname: Eike
    lastname: Budinger
    affiliation: 'Leibniz Institute for Neurobiology (LIN), Combinatorial Neuroimaging Core Facility (CNI), Magdeburg, Germany'
    id: ''
  -
    firstname: Santiago
    lastname: Canals
    affiliation: 'Instituto de Neurociencias, CSIC/UMH, San Juan de Alicante, 03550 Alicante, Spain'
    id: ''
  -
    firstname: Silvia De
    lastname: Santis
    affiliation: 'Instituto de Neurociencias, CSIC/UMH, San Juan de Alicante, 03550 Alicante, Spain'
    id: ''
  -
    firstname: Roberta Diaz
    lastname: Brinton
    affiliation: 'Center for Innovation in Brain Science, University of Arizona, Tucson, AZ, USA'
    id: ''
  -
    firstname: Rick M.
    lastname: Dijkhuizen
    affiliation: 'Biomedical MR Imaging and Spectroscopy group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands'
    id: ''
  -
    firstname: Elisenda
    lastname: Eixarch
    affiliation: 'BCNatal Fetal Medicine Research Center (Hospital Clínic and Hospital Sant Joan de Déu), Universitat de Barcelona; Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); and Centre for Biomedical Research on Rare Diseases (CIBER-ER), Spain'
    id: ''
  -
    firstname: Gianluigi
    lastname: Forloni
    affiliation: 'Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Neuroscience, Milan, Italy'
    id: ''
  -
    firstname: Joanes
    lastname: Grandjean
    affiliation: 'Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands, and Department of Medical Imaging, Radboud University Medical Center, Nijmegen, The Netherlands'
    id: ''
  -
    firstname: Khan
    lastname: Hekmatyar
    affiliation: 'Center for Behavioral Neuroscience, Neuroscience Institute, Advanced Translational Imaging Facility, Georgia State University, Atlanta, Georgia, USA'
    id: ''
  -
    firstname: Russell E.
    lastname: Jacobs
    affiliation: 'Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA'
    id: ''
  -
    firstname: Ileana
    lastname: Jelescu
    affiliation: 'Department of Radiology, Lausanne University Hospital (CHUV), Lausanne, Switzerland, and CIBM Center for Biomedical Imaging, Lausanne, Switzerland'
    id: ''
  -
    firstname: Nyoman D.
    lastname: Kurniawan
    affiliation: 'Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Australia'
    id: ''
  -
    firstname: Giuseppe
    lastname: Lembo
    affiliation: 'IRCCS INM Neuromed, Department of AngioCardioNeurology and Translational Medicine, Pozzilli, Italy, and Sapienza University of Rome, Department of Molecular Medicine, Rome, Italy'
    id: ''
  -
    firstname: Dario Livio
    lastname: Longo
    affiliation: 'Institute of Biostructures and Bioimaging (IBB), National Research Council of Italy (CNR), Turin, Italy'
    id: ''
  -
    firstname: Naomi S.
    lastname: Sta Maria
    affiliation: 'Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA'
    id: ''
  -
    firstname: Edoardo
    lastname: Micotti
    affiliation: 'Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Neuroscience, Milan, Italy'
    id: ''
  -
    firstname: Emma
    lastname: Muñoz-Moreno
    affiliation: 'MRI Core Facility, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain'
    id: ''
  -
    firstname: Pedro
    lastname: Ramos-Cabrer
    affiliation: 'Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain'
    id: ''
  -
    firstname: Wilfried
    lastname: Reichardt
    affiliation: 'Medical Physics, Department of Radiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany'
    id: ''
  -
    firstname: Guadalupe
    lastname: Soria
    affiliation: 'CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, and Laboratory of Surgical and Experimental Neuroanatomy, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, Barcelona, Spain'
    id: ''
  -
    firstname: Giovanna D.
    lastname: Ielacqua
    affiliation: 'Preclinical Research Center (PRC), Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany'
    id: ''
  -
    firstname: Markus
    lastname: Aswendt
    affiliation: 'University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Neurology, Cologne, Germany '
    id: 'ORCID:0000-0003-1423-0934'
# A title to describe the published resource.
title: "Automated quality control of small animal MR neuroimaging data"


# Additional information about the resource, e.g., a brief abstract.
description: "MRI is a valuable tool for studying brain structure and function in animal and clinical studies. With the growth of public MRI repositories, access to data has finally become easier. However, filtering large data sets for potential poor quality outliers can be a challenge. We present AIDAqc, a machine learning-assisted automated Python-based command-line tool for the quality assessment of small animal MRI data. Quality control features include signal-to-noise ratio (SNR), temporal SNR, and motion. All features are automatically calculated and no regions of interest are needed. Automated outlier detection is based on the combination of interquartile range and the machine learning methods one-class support vector machine, isolation forest, local outlier factor, and elliptic envelope. AIDAqc was challenged in a large heterogeneous dataset collected from 18 international laboratories, including data from mice, rats, rabbits, hamsters, and gerbils, obtained with different hardware and at different field strengths. The results show that the manual inter-rater variability (mean Fleiss Kappa score 0.17) is high when identifying poor quality data. A direct comparison of AIDAqc results therefore showed only low to moderate concordance. In a manual post-hoc validation of AIDAqc output, agreement was high (>70%). The outlier data can have a significant impact on further post-processing, as shown in representative functional and structural connectivity analysis. In summary, this pipeline optimized for small animal MRI provides researchers with a valuable tool to efficiently and effectively assess the quality of their MRI data, which is essential for improved reliability and reproducibility."

# List of keywords the resource should be associated with.
# Give as many keywords as possible, to make the resource findable.
keywords:
  - Quality control
  - MRI
  - Preclinical imaging
  - DataLad
  - Animal models
  - Imaging
  - fMRI analysis
  - Machine learning
  - Motion analysis
  - Functional imaging
  - Diffusion weighted imaging
  - Image quality assessment

# License information for this resource. Please provide the license name and/or a link to the license.
# Please add also a corresponding LICENSE file to the repository.
license:
  name: "CC BY-NC-SA 4.0"
  url: "https://creativecommons.org/licenses/by-nc-sa/4.0/"

# Funding information for this resource.
# Separate funder name and grant number by semicolon.
# Funding information for this resource.
# Separate funder name and grant number by semicolon.
funding:
  - "DFG; 431549029 – SFB 1451"
  - "Friebe Foundation; T0498/28960/16"
  - "Italian Minister of Health; RRC-2016-2361095, RRC-2017-2364915, RRC-2018-2365796, RCR-2019-23669119_001, RCR 2020-23670067"
  - "Ministry of Economy and Finance; CCR-2017-23669078"
  - "Australian National Imaging Facility (NIF)"
  - "Queensland NMR Network (QNN)"
  - "European Union’s Horizon 2020 research and innovation program EOSC-Life—Providing an open collaborative space for digital biology in Europe; Grant agreement No 824087"
  - "Italian Ministry for Education and Research (FOE funding to the Euro-BioImaging Multi-Modal Molecular Imaging Italian Node)"
  - "NIH S10 OD025016;R01AG057931"
  - "NIH/National Institute on Aging P01AG026572"
  - "Center for Innovation in Brain Science"
  - "Spanish Research Agency; Grant PID2020-118546RB-I00"
  - "Horizon Europe programs CANDY under grant agreement nos. 847818"
  - "Dutch Research Council; OCENW.KLEIN.334"
  - "Spanish Research Agency; PID2021-128158NB-C21, PID2021-128909NA-I00, CEX2021-001165-S"
  - "Spanish Generalitat Valenciana Government; PROMETEO/2019/015, CIDEGENT/2021/015"
  - "la Caixa Foundation; fellowship code LCF/BQ/DI18/11660067"
  - "Marie Skłodowska-Curie-COFUND agreement; Grant No. 713673"
  - "SNSF Eccellenza PCEFP2_194260"
  - "CIBM Center for Biomedical Imaging of the UNIL, CHUV, EPFL, HUG, and UNIGE"
  - "DFG project BO 4484/2-1 and EXC-2049-390688087 NeuroCure"
  - "German Federal Ministry of Education and Research (BMBF) under the ERA-NET NEURON scheme; 01EW1811 and 01EW2305"
  - "Charité 3R | Replace, Reduce, Refine"
references:
  -
    id: "doi:tba"
    reftype: "IsSupplementTo"
    citation: "Kalantari, Aref et. al 2024, Automated quality control of small animal MR neuroimaging data, Imaging Neuroscience, first submission on 23.12.2023"
    
# Resource type. Default is Dataset, other possible values are Software, Image, Text.
resourcetype: Dataset

# Do not edit or remove the following line
templateversion: 1.2