Brief intro to Open Neuroimaging Verena Heise MRI

Brief intro to Open Neuroimaging Verena Heise MRI grad programme

What is Open Science?

Andreas E. Neuhold, Six Open Science Principles, https: //en. wikipedia. org/wiki/Open_science

Why do I care?

Fang and Casadevall, Infection and Immunity, 2011, 79: 3855 -3859

What can we do?

Open Science https: //osf. io/tvyxz/wiki/home/

Open Science https: //osf. io/tvyxz/wiki/home/

Open Data • WIN Open imaging data strategy is work in progress • Organise data according to BIDS format: http: //bids. neuroimaging. io/ • Publish summary stats results on https: //neurovault. org/

Open Science https: //osf. io/tvyxz/wiki/home/

Open Materials • FSL • Share your MR protocols • Share your tasks • Publish the analysis scripts (ALL of them and make them readable ) => WIN gitlab site (git. fmrib. ox. ac. uk)

Open Science https: //osf. io/tvyxz/wiki/home/

Pre-registration • Write up your hypothesis, study design and detailed analysis pipeline (introduction and methods) • Pre-register it online (e. g. on OSF) or use registered report • Registered report means your study will be published IRRESPECTIVE of results, purely based on scientific merit => you get feedback before you collect the data => you can put it on your CV before you have finished the study • More info on pre-registration: https: //tomstafford. staff. shef. ac. uk/? p=573 and registered reports: https: //cos. io/rr/

Pre-registration Munafo et al. , A manifesto for reproducible science, https: //www. nature. com/articles/s 41562 -016 -0021

Open Science Open Reporting

Open Reporting • Publish ALL the analyses you did (pre-registered and exploratory) • Publish ALL results (not just “significant” ones) • Publish according to best practice guidelines

Open Reporting

Open Reporting • Publish ALL the analyses you did (pre-registered and exploratory) • Publish ALL results (not just “significant” ones) • Publish according to best practice guidelines • Use preprints • Publish Open Access

Open Reporting https: //git. fmrib. ox. ac. uk/open-science/Documentation/wikis/home

Good Scientific Practice

Ask the right question • Do a proper literature review, look for systematic reviews and meta-analyses, where are the gaps? • Speak to clinicians • Talk to your colleagues • Via patient and public involvement (PPI) initiatives, e. g. James Lind Alliance • Find out priority areas for funders and policy makers

Good Scientific Practice

Design your study properly

Statistical power

Statistical power • Median statistical power in neuroscience: 21% • Median statistical power in animal studies: between 18 – 31% • Median statistical power in neuroimaging: 8% => chance of false negative = 1 -power => “the likelihood that any nominally significant finding actually reflects a true effect is small” (low positive predictive value)

Sample size calculation - example • Effect size = Cohen’s d of 0. 5 (medium effect) • Statistical power to find effect = 90% • alpha = 0. 05 • One sample one-tailed t test Þ 36 participants • Independent groups two-tailed t test Þ 86 participants per group

Sample size calculators • General statistical power: http: //www. gpower. hhu. de/en. html • f. MRI power tools: http: //neuropowertools. org/ http: //fmripower. org/

Do you need to collect new data? • UK Biobank • Human Connectome Project • Many other collaborations, e. g. in disease-specific areas

Good Scientific Practice Sidney Harris, What’s so funny about Science? (1977)

Reproducible workflows • Keep an electronic labbook • Script as much as you can • Helpful tools: R Studio: https: //www. rstudio. com/ R Markdown: https: //rmarkdown. rstudio. com/ Python: https: //www. python. org/ Jupyter Notebook: https: //jupyter. org/

Reproducible measures • Validity (Can I get the right answer? ) • Reliability (Can I get the same answer twice? ) Reliable Not Valid Not reliable Not valid Both reliable and valid

Robust Research - summary • Open Science • Data • Materials • Reporting (and pre-registration) • Good Scientific Practice • Relevant research question • Statistical power and procedures • Reproducible workflows • Reproducible measures (validity, reliability, QC procedures)

Robust Research - summary PRE-REGISTER (or use Registered Reports)

https: //en. wikipedia. org/wiki/The_Scream

Want to know more? • WIN Open Imaging website coming soon • Journal club @ New Radcliffe House, Fridays at 1 pm, @Reproducibili. T • Seminar series, Wednesdays at 4. 30 pm: http: //users. ox. ac. uk/~phys 1213/Repro. At. ASC. html • Software/ data carpentry workshops: https: //rroxford. github. io • Become a WIN Open Imaging Ambassador • Ask me (slides on https: //osf. io/5 rfm 6/)

Questions or comments? verena. heise@ndph. ox. ac. uk