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Visual QC Protocol for FreeSurfer Cortical Parcellations from Anatomical MRI

View ORCID ProfilePradeep Reddy Raamana, Athena Theyers, Tharushan Selliah, Piali Bhati, Stephen R. Arnott, Stefanie Hassel, Nuwan D. Nanayakkara, Christopher J. M. Scott, Jacqueline Harris, Mojdeh Zamyadi, Raymond W. Lam, Roumen Milev, Daniel J. Müller, Susan Rotzinger, Benicio N. Frey, Sidney H Kennedy, Sandra E. Black, Anthony Lang, Mario Masellis, Sean Symons, Robert Bartha, Glenda M MacQueen, The CAN-BIND Investigator Team, The ONDRI Investigators, Stephen C. Strother
doi: https://doi.org/10.1101/2020.09.07.286807
Pradeep Reddy Raamana
1Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
20Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA
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  • ORCID record for Pradeep Reddy Raamana
  • For correspondence: raamanap@pitt.edu
Athena Theyers
1Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
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Tharushan Selliah
1Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
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Piali Bhati
1Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
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Stephen R. Arnott
1Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
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Stefanie Hassel
3Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
4Mathison Centre for Mental Health Research and Education, University of Calgary, Calgary, AB, Canada
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Nuwan D. Nanayakkara
17Centre for Functional and Metabolic Mapping, Robarts Research Institute, Department of Medical Biophysics, University of Western Ontario, London, ON, Canada
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Christopher J. M. Scott
13LC Campbell Cognitive Neurology Research, Hurvitz Brain Sciences Program, Sunnybrook Health Sciences
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Jacqueline Harris
5Department of Computing Science, University of Alberta, Edmonton, AB, Canada
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Mojdeh Zamyadi
1Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
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Raymond W. Lam
6Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
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Roumen Milev
7Departments of Psychiatry and Psychology, Queen’s University and Providence Care Hospital, Kingston, ON, Canada
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Daniel J. Müller
8Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
9Department of Psychiatry, University of Toronto, Toronto, ON, Canada
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Susan Rotzinger
9Department of Psychiatry, University of Toronto, Toronto, ON, Canada
10Department of Psychiatry, Krembil Research Centre, University Health Network, Toronto, ON, Canada
11Department of Psychiatry, St. Michael’s Hospital, University of Toronto, Toronto, ON, Canada
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Benicio N. Frey
18Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
19Mood Disorders Program, St. Joseph’s Healthcare Hamilton, ON, Canada
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Sidney H Kennedy
9Department of Psychiatry, University of Toronto, Toronto, ON, Canada
10Department of Psychiatry, Krembil Research Centre, University Health Network, Toronto, ON, Canada
11Department of Psychiatry, St. Michael’s Hospital, University of Toronto, Toronto, ON, Canada
12Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON, Canada
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Sandra E. Black
13LC Campbell Cognitive Neurology Research, Hurvitz Brain Sciences Program, Sunnybrook Health Sciences
14Department of Medicine (Neurology), University of Toronto, ON, Canada
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Anthony Lang
14Department of Medicine (Neurology), University of Toronto, ON, Canada
15Edmond J Safra Program in Parkinson’s Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, ON, Canada
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Mario Masellis
13LC Campbell Cognitive Neurology Research, Hurvitz Brain Sciences Program, Sunnybrook Health Sciences
14Department of Medicine (Neurology), University of Toronto, ON, Canada
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Sean Symons
16Department of Medical Imaging, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
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Robert Bartha
17Centre for Functional and Metabolic Mapping, Robarts Research Institute, Department of Medical Biophysics, University of Western Ontario, London, ON, Canada
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Glenda M MacQueen
3Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
4Mathison Centre for Mental Health Research and Education, University of Calgary, Calgary, AB, Canada
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Stephen C. Strother
1Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada
2Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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Abstract

Quality control of morphometric neuroimaging data is essential to improve reproducibility. Owing to the complexity of neuroimaging data and subsequently the interpretation of their results, visual inspection by trained raters is the most reliable way to perform quality control. Here, we present a protocol for visual quality control of the anatomical accuracy of FreeSurfer parcellations, based on an easy-to-use open source tool called VisualQC. We comprehensively evaluate its utility in terms of error detection rate and inter-rater reliability on two large multi-site datasets, and discuss site differences in error patterns. This evaluation shows that VisualQC is a practically viable protocol for community adoption.

Competing Interest Statement

The author(s) declared the following potential conflicts of interest with respect to the research, authorship, and/or publication of this article. Various datasets and programs referred to here received funding from Lundbeck, Bristol-Myers Squibb, Pfizer, and Servier. The funders were not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication. RM has received consulting and speaking honoraria from AbbVie, Allergan, Janssen, KYE, Lundbeck, Otsuka, and Sunovion, and research grants from CAN-BIND, CIHR, Janssen, Lallemand, Lundbeck, Nubiyota, OBI, and OMHF. RL has received honoraria or research funds from Allergan, Asia-Pacific Economic Cooperation, BC Leading Edge Foundation, CIHR, CANMAT, Canadian Psychiatric Association, Hansoh, Healthy Minds Canada, Janssen, Lundbeck, Lundbeck Institute, MITACS, Myriad Neuroscience, Ontario Brain Institute, Otsuka, Pfizer, St. Jude Medical, University Health Network Foundation, and VGH-UBCH Foundation. SCS is the Chief Scientific Officer of ADMdx, Inc., which receives NIH funding, and he currently has research grants from Brain Canada, Canada Foundation for Innovation (CFI), Canadian Institutes of Health Research (CIHR), and the Ontario Brain Institute in Canada. BF has received a research grant from Pfizer. SK has received research funding or honoraria from Abbott, Alkermes, Allergan, Bristol-Myers Squibb, Brain Canada, Canadian Institutes for Health Research (CIHR), Janssen, Lundbeck, Lundbeck Institute, Ontario Brain Institute (OBI), Ontario Research Fund (ORF), Otsuka, Pfizer, Servier, Sunovion, and Xian-Janssen. GM has received consultancy/speaker fees from Lundbeck, Pfizer, Johnson & Johnson and Janssen.

Footnotes

  • much improved discussion; additional data visualizations and clarifications to ensure accurate interpretation

  • https://www.github.com/raamana/visualqc

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted December 14, 2021.
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Visual QC Protocol for FreeSurfer Cortical Parcellations from Anatomical MRI
Pradeep Reddy Raamana, Athena Theyers, Tharushan Selliah, Piali Bhati, Stephen R. Arnott, Stefanie Hassel, Nuwan D. Nanayakkara, Christopher J. M. Scott, Jacqueline Harris, Mojdeh Zamyadi, Raymond W. Lam, Roumen Milev, Daniel J. Müller, Susan Rotzinger, Benicio N. Frey, Sidney H Kennedy, Sandra E. Black, Anthony Lang, Mario Masellis, Sean Symons, Robert Bartha, Glenda M MacQueen, The CAN-BIND Investigator Team, The ONDRI Investigators, Stephen C. Strother
bioRxiv 2020.09.07.286807; doi: https://doi.org/10.1101/2020.09.07.286807
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Visual QC Protocol for FreeSurfer Cortical Parcellations from Anatomical MRI
Pradeep Reddy Raamana, Athena Theyers, Tharushan Selliah, Piali Bhati, Stephen R. Arnott, Stefanie Hassel, Nuwan D. Nanayakkara, Christopher J. M. Scott, Jacqueline Harris, Mojdeh Zamyadi, Raymond W. Lam, Roumen Milev, Daniel J. Müller, Susan Rotzinger, Benicio N. Frey, Sidney H Kennedy, Sandra E. Black, Anthony Lang, Mario Masellis, Sean Symons, Robert Bartha, Glenda M MacQueen, The CAN-BIND Investigator Team, The ONDRI Investigators, Stephen C. Strother
bioRxiv 2020.09.07.286807; doi: https://doi.org/10.1101/2020.09.07.286807

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