Collection of all datasets used to develop AIDAqc

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README.md

Collection of Resources for AIDAqc Pipeline

This repository contains various resources related to the AIDAqc pipeline used in the following Publication: Automated quality control of small animal MR neuroimaging data, DOI: tbd.

Repository Structure:

  • code/: Here, you can find all the code used for this publication. Detailed information is available in the README of the code folder.

  • input/: This folder contains all datasets used in the publication.

  • output/: Within this directory, you'll locate the final results generated by the AIDAqc pipeline for each dataset. Detailed information for each dataset's output can be found in their respective subfolders.

  • docs/: Additional documentation related to this project, including extra resources in the form of a README file within this folder.

Additional Information:

This structured dataset was created with reference to the following publication:

DOI:10.1038/s41597-023-02242-8

If you have any questions or require further assistance, please do not hesitate to reach out to us. Contact us via email at markus.aswendt@uk-koeln.de or aref.kalantari-sarcheshmeh@uk-koeln.de.

datacite.yml
Title Automated quality control of small animal MR neuroimaging data
Authors Kalantari,Aref;University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Neurology, Cologne, Germany ;ORCID:0000-0003-3050-0930
Shahbazi,Mehrab;Hamedan University of Technology, Faculty of Medical Engineering, Hamedan, Iran
Schneider,Marc;University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Neurology, Cologne, Germany
Frazão,Victor Vera;University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Neurology, Cologne, Germany
Bhattrai,Avnish;Center for Innovation in Brain Science, University of Arizona, Tucson, AZ, USA
Carnevale,Lorenzo;IRCCS INM Neuromed, Department of AngioCardioNeurology and Translational Medicine, Pozzilli, Italy
Diao,Yujian;Department of Radiology, Lausanne University Hospital (CHUV), Lausanne, Switzerland, and CIBM Center for Biomedical Imaging, Lausanne, Switzerland
Franx,Bart A. A.;Biomedical MR Imaging and Spectroscopy group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
Gammaraccio,Francesco;Molecular Imaging Center, Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
Goncalves,Lisa-Marie;Leibniz Institute for Neurobiology (LIN), Combinatorial Neuroimaging Core Facility (CNI), Magdeburg, Germany
Lee,Susan;Center for Behavioral Neuroscience, Neuroscience Institute, Advanced Translational Imaging Facility, Georgia State University, Atlanta, Georgia, USA
van Leeuwen,Esther M.;Biomedical MR Imaging and Spectroscopy group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
Michalek,Annika;Leibniz Institute for Neurobiology (LIN), Combinatorial Neuroimaging Core Facility (CNI), Magdeburg, Germany
Mueller,Susanne;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
Olvera,Alejandro Rivera;Ikerbasque, Basque Foundation for Science, Bilbao, Spain
Padro,Daniel;Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
Raikes,Adam C.;Center for Innovation in Brain Science, University of Arizona, Tucson, AZ, USA
Selim,Mohamed Kotb;Instituto de Neurociencias, CSIC/UMH, San Juan de Alicante, 03550 Alicante, Spain
van der Toorn,Annette;Biomedical MR Imaging and Spectroscopy group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
Varriano,Federico;Laboratory of Surgical and Experimental Neuroanatomy, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, Barcelona, Spain
Vrooman,Roël;Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
Wenk,Patricia;Leibniz Institute for Neurobiology (LIN), Combinatorial Neuroimaging Core Facility (CNI), Magdeburg, Germany
Albers,H Elliott;Center for Behavioral Neuroscience, Neuroscience Institute, Advanced Translational Imaging Facility, Georgia State University, Atlanta, Georgia, USA
Boehm-Sturm,Philipp;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
Budinger,Eike;Leibniz Institute for Neurobiology (LIN), Combinatorial Neuroimaging Core Facility (CNI), Magdeburg, Germany
Canals,Santiago;Instituto de Neurociencias, CSIC/UMH, San Juan de Alicante, 03550 Alicante, Spain
Santis,Silvia De;Instituto de Neurociencias, CSIC/UMH, San Juan de Alicante, 03550 Alicante, Spain
Brinton,Roberta Diaz;Center for Innovation in Brain Science, University of Arizona, Tucson, AZ, USA
Dijkhuizen,Rick M.;Biomedical MR Imaging and Spectroscopy group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
Eixarch,Elisenda;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
Forloni,Gianluigi;Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Neuroscience, Milan, Italy
Grandjean,Joanes;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
Hekmatyar,Khan;Center for Behavioral Neuroscience, Neuroscience Institute, Advanced Translational Imaging Facility, Georgia State University, Atlanta, Georgia, USA
Jacobs,Russell E.;Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
Jelescu,Ileana;Department of Radiology, Lausanne University Hospital (CHUV), Lausanne, Switzerland, and CIBM Center for Biomedical Imaging, Lausanne, Switzerland
Kurniawan,Nyoman D.;Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Australia
Lembo,Giuseppe;IRCCS INM Neuromed, Department of AngioCardioNeurology and Translational Medicine, Pozzilli, Italy, and Sapienza University of Rome, Department of Molecular Medicine, Rome, Italy
Longo,Dario Livio;Institute of Biostructures and Bioimaging (IBB), National Research Council of Italy (CNR), Turin, Italy
Sta Maria,Naomi S.;Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
Micotti,Edoardo;Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Neuroscience, Milan, Italy
Muñoz-Moreno,Emma;MRI Core Facility, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
Ramos-Cabrer,Pedro;Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
Reichardt,Wilfried;Medical Physics, Department of Radiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
Soria,Guadalupe;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
Ielacqua,Giovanna D.;Preclinical Research Center (PRC), Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
Aswendt,Markus;University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Neurology, Cologne, Germany ;ORCID:0000-0003-1423-0934
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.
License CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/)
References Kalantari, Aref et. al 2024, Automated quality control of small animal MR neuroimaging data, Imaging Neuroscience, first submission on 23.12.2023 [doi:tba] (IsSupplementTo)
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
Keywords Quality control
MRI
Preclinical imaging
DataLad
Animal models
Imaging
fMRI analysis
Machine learning
Motion analysis
Functional imaging
Diffusion weighted imaging
Image quality assessment
Resource Type Dataset