Panel: Towards reproducible brain imaging research
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- Kerrie Nicholson
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1 WIN Conference, 24th January 2017 Panel: Towards reproducible brain imaging research Camille Maumet, Alexander Bowring, Thomas Nichols Neuroimaging Statistics, IDH, University of Warwick, UK
2 WIN Conference, 24th January 2017 Introduction to reproducible neuroimaging research Current practices & limitations Camille Maumet Neuroimaging Statistics, IDH, University of Warwick, UK cmaumet cmaumet
3 Outline Introduction to reproducible neuroimaging research Reproducible research? Levels of reproducibility Tools available for reproducible neuroimaging & future
4 Reproducible research?
5 Reproducibility 3
6 Lack of reproducibility can be due to... No effect Low power Weak experimental design Publication bias Analytical flexibility (p-hacking) Errors (e.g. software bugs) Statistics Programming Not enough details reported Underspecified methods Reporting Reproducibility and Reliability of Biomedical Research The Academy of Medical Sciences
7 Levels of reproducibility
8 Levels of reproducibility Same lab Same settings Different lab Same settings Different lab Different settings 6
9 Levels of reproducibility Same lab Same settings Robustness Requires: Systematic data organisation and description of experiment (e.g. scripting) Different lab Same settings Validation Requires: Detailed description of the experiment (tools, scripts) and availability of the data Different lab Different settings Generalisation Requires: High-level description of the research hypothesis (research paper) 6
10 Levels of reproducibility Same lab Same settings Robustness Requires: Systematic data organisation and description of experiment (e.g. scripting) Different lab Same settings Validation Requires: Detailed description of the experiment (tools, scripts) and availability of the data Different lab Different settings Generalisation Requires: High-level description of the research hypothesis (research paper) Build on hypothesis 6
11 Levels of reproducibility Same lab Same settings Robustness Requires: Systematic data organisation and description of experiment (e.g. scripting) Different lab Same settings Validation Requires: Detailed description of the experiment (tools, scripts) and availability of the data Build on hypothesis Different lab Different settings Generalisation Requires: High-level description of the research hypothesis (research paper) Build on hypothesis 6
12 Levels of reproducibility Same lab Same settings Robustness Requires: Systematic data organisation and description of experiment (e.g. scripting) Build on hypothesis Different lab Same settings Validation Requires: Detailed description of the experiment (tools, scripts) and availability of the data Build on hypothesis Different lab Different settings Generalisation Requires: High-level description of the research hypothesis (research paper) Build on hypothesis 6
13 Levels of reproducibility Same lab Same settings Robustness Requires: Systematic data organisation and description of experiment (e.g. scripting) Different lab Same settings Validation Requires: Detailed description of the experiment (tools, scripts) and availability of the data Build on hypothesis Build on hypothesis Project extension Methods/Data re-use Different lab Different settings Generalisation Requires: High-level description of the research hypothesis (research paper) Build on hypothesis 6
14 Tools for reproducible neuroimaging
15 Neuroimaging analysis pipeline Raw data Pre-processing Pre-processed data Analysis Results Publication Publication 8
16 Neuroimaging analysis pipeline Raw data Pre-processing Sharing of experimental details Data sharing Pre-processed data Analysis Results Publication Publication 8
17 Data availability Structured data organisation Data sharing Raw data Pre-processed data Results Publication 9
18 Data availability Structured data organisation Data sharing Raw data Pre-processed data Results Publication 9
19 Data availability Structured data organisation Data sharing Raw data Pre-processed data Results Publication 9
20 Data availability Structured data organisation Data sharing Raw data Pre-processed data?????? Results??? Publication 9
21 Publishing the details of the experiment Structured description of the experiment Sharing of experimental details Acquisition Pre-processing & statistical analysis Figures & tables 10
22 Publishing the details of the experiment Structured description of the experiment Sharing of experimental details Acquisition COBIDAS Analysis tools Pre-processing & statistical analysis Pipelining engines Docker containers Custom scripts Figures & tables notebooks 10
23 Publishing the details of the experiment Structured description of the experiment Sharing of experimental details Acquisition COBIDAS Analysis tools Pre-processing & statistical analysis Pipelining engines Docker containers Custom scripts Figures & tables notebooks 10
24 Publishing the details of the experiment Structured description of the experiment Acquisition Sharing of experimental details??? Machine readable COBIDAS Compliance w/ guidelines Analysis tools Pre-processing & statistical analysis Pipelining engines Harmonisation Docker containers Training Custom scripts Figures & tables notebooks 10
25 Panel Towards reproducible brain imaging research Introduction: current practices and limitations Camille Maumet COBIDAS: improving reporting guidelines Thomas Nichols Investigating reproducibility across neuroimaging software pipelines Alexander Bowring 11
26 Q&A
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