Merge remote-tracking branch 'origin/master'

README.md

@@ -1,16 +1,18 @@
+
 # Collection of Resources for AIDAqc Pipeline
 
-This repository contains various resources related to the [AIDAqc pipeline](git@github.com:Aswendt-Lab/AIDAqc.git) used in the following Publication: ***Automated quality control of small animal MR neuroimaging data***, DOI: tbd. Each subsection for code, input, output, and docs provides more detailed information for each folder or file.
+
+This repository contains various resources related to the [AIDAqc pipeline](https://github.com/Aswendt-Lab/AIDAqc) 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 and other necessary data. More detailed information regarding each dataset can be found in the respective subfolders.
+- `input/`: This folder contains all datasets used in the publication.
 
-- `output/`: Within this directory, you'll locate the final results generated by the [AIDAqc](https://github.com/Aswendt-Lab/AIDAqc) pipeline for each dataset. Detailed information for each dataset's output can be found in their respective subfolders.
+- `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/`: For additional documentation related to this project, including extra resources, you can access it via this [link](https://github.com/Aswendt-Lab/MRI_Standardization_AIDAqc) or through the README file within this folder.
+- `docs/`: Additional documentation related to this project, including extra resources in the form of a README file within this folder.
 
 ## Additional Information:
 
@@ -18,4 +20,7 @@ This structured dataset was created with reference to the following publication:
 
 [DOI:10.1038/s41597-023-02242-8](https://www.nature.com/articles/s41597-023-02242-8)
 
-If you have any questions or need further assistance, please feel free to contact us.  
+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](mailto:markus.aswendt@uk-koeln.de) or [aref.kalantari-sarcheshmeh@uk-koeln.de](mailto:aref.kalantari-sarcheshmeh@uk-koeln.de).
+
+
+<img align="right" src="/docs/AIDA_Logo_wide.001.png" width="200">

datacite.yml

@@ -6,30 +6,259 @@
 # The main researchers involved. Include digital identifier (e.g., ORCID)
 # if possible, including the prefix to indicate its type.
 authors:
-  -
-    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'
   -
     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: "This dataset is a super-dataset containing all datasets used to develop the AIDAqc pipeline and corresponds to the following Publication (DOI): tbd"
+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."
 
-# Lit of keywords the resource should be associated with.
+# List of keywords the resource should be associated with.
 # Give as many keywords as possible, to make the resource findable.
 keywords:
-  - Quality-control
+  - Quality control
   - MRI
-  - Preclinical-imaging
+  - 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.
@@ -37,28 +266,40 @@ license:
   name: "CC BY-NC-SA 4.0"
   url: "https://creativecommons.org/licenses/by-nc-sa/4.0/"
 
-
-
-## Optional Fields
-
+# 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"
-  
-
-
-# Related publications. reftype might be: IsSupplementTo, IsDescribedBy, IsReferencedBy.
-# Please provide digital identifier (e.g., DOI) if possible.
-# Add a prefix to the ID, separated by a colon, to indicate the source.
-# Supported sources are: DOI, arXiv, PMID
-# In the citation field, please provide the full reference, including title, authors, journal etc.
+  - "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: "Aref Kalantari, Mehrab Shahbazi, Marc Schneider, Victor Vera Frazão, Avnish Bhattrai, Lorenzo Carnevale, Yujian Diao, Bart A. A. Franx, Francesco Gammaraccio, Lisa-Marie Goncalves, Susan Lee, Esther M. van Leeuwen, Annika Michalek, Susanne Mueller, Alejandro Rivera Olvera, Daniel Padro, Adam C. Raikes, Mohamed Kotb Selim, Annette van der Toorn, Federico Varriano, Roël Vrooman, Patricia Wenk, H Elliott Albers, Philipp Boehm-Sturm, Eike Budinger, Santiago Canals, Silvia De Santis, Roberta Diaz Brinton, Rick M. Dijkhuizen, Elisenda Eixarch, Gianluigi Forloni, Joanes Grandjean, Khan Hekmatyar, Russell E. Jacobs, Ileana Jelescu, Nyoman D. Kurniawan, Giuseppe Lembo, Dario Livio Longo, Naomi S. Sta Maria, Edoardo Micotti, Emma Muñoz-Moreno, Pedro Ramos-Cabrer, Wilfried Reichardt, Guadalupe Soria, Giovanna D. Ielacqua, Markus Aswendt"
+    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