diff --git a/docs/assets/fmriprep-bootcamp-geneva2024/day1-01-fmriprep-primer/images/reproducible-definition-grid.svg b/docs/assets/fmriprep-bootcamp-geneva2024/day1-01-fmriprep-primer/images/reproducible-definition-grid.svg new file mode 100644 index 0000000..1b80c01 --- /dev/null +++ b/docs/assets/fmriprep-bootcamp-geneva2024/day1-01-fmriprep-primer/images/reproducible-definition-grid.svg @@ -0,0 +1,4940 @@ + + + +Reproducible Definition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Reproducible Definition2023-05-03CC-BY 4.0The Turing Wayscriberia, da5nsy, Richard J. Actonscriberia http://www.scriberia.co.uk/https://github.com/the-turing-way/the-turing-way/blob/main/book/website/figures/reproducible-definition-grid.svgEnglish (UK)reproducible; definition; replicable; generalisable; robust; data analysis; open science; open life science; the turing wayAlt Text: Grid with the characteristics of: Reproducible; same data, same analysis. Replicable; different data, same analysis. Robust; same data, different analysis. And generalisable; different data, different analysis; Research diff --git a/docs/assets/fmriprep-bootcamp-geneva2024/day1-01-fmriprep-primer/index.html b/docs/assets/fmriprep-bootcamp-geneva2024/day1-01-fmriprep-primer/index.html index d52e046..c98c677 100644 --- a/docs/assets/fmriprep-bootcamp-geneva2024/day1-01-fmriprep-primer/index.html +++ b/docs/assets/fmriprep-bootcamp-geneva2024/day1-01-fmriprep-primer/index.html @@ -46,11 +46,19 @@ font-size: 0.7em; } li p { line-height: 1.25em; } - + .remark-slide-content>p { margin-left: 60px; } .remark-slide-content>ul { margin-left: 60px; } .remark-slide-content>ul li { margin-left: 0.8em; } + .no-bullet > ul { + list-style-type: none; + padding-left: 0; + } + + .no-bullet > ul > li > ul { + padding-left: 2.8em; + } .red { color: #fa0000; } .blue { color: #0000fa; } @@ -555,23 +563,32 @@ --- -# Reproducibility - -.boxed-content[


-.center[ -![](https://book.the-turing-way.org/_images/reproducible-matrix.jpg) -.pull-right[(from [The Turing Way](https://book.the-turing-way.org/reproducible-research/overview/overview-definitions#table-of-definitions-for-reproducibility))] +
+
+
+ +.boxed-content[ +.large.center[ +# Processing and reproducibility ] +.larger.center.gray-text[How do they interact? Why *fMRIPrep*? +]] + +--- + +.center[ +HPC +.small[ +*The Turing Way project* illustration by Scriberia. Used under a CC-BY 4.0 licence. doi:10.5281/zenodo.3332807.] ] --- # Reproducibility: increasing measurements' reliability -

.large[ @@ -581,12 +598,15 @@ Standardize the measurement procedure - .gray-text[Reduce variance (potentially at the cost of bias)] + .gray-text[Reduce methodology variance (potentially at the cost of bias)] ]
-.center.larger[.larger[Neither ensures the *validity* of the measurement]] +.center.large[ +Both strategies *reduce the variance* of the measurement. + +Neither ensures the *validity* of the measurement] --- @@ -599,7 +619,7 @@ ] .larger[ -* NARPS ([Botvinik-Nezer et al., 2020](https://doi.org/10.1038/s41586-020-2314-9)): single dataset, 70 teams, 9 *ex-ante* hypotheses. +* NARPS ([Botvinik-Nezer et al., 2020](https://doi.org/10.1038/s41586-020-2314-9)): single dataset, 70 teams, 9 ex-ante hypotheses. Striking analytical variability (even with teams using same preprocessing) @@ -755,7 +775,7 @@ * Use *Nipype* to abstract from tool details and construct modular workflows ] -.large[ Standardization and best-practices] +.large[ Standardization and best-practices — [check (Esteban, 2024)](https://doi.org/10.31219/osf.io/42bsu)] .larger[ * BIDS (inputs), BIDS Derivatives (outputs), BIDS Apps (architecture). * Containers, versioning, LTS, open-source, CI/CD, etc. @@ -789,6 +809,28 @@ ] +--- + +# Standardization in the research workflow + +.boxed-content[ +
+.center[ +workflow +] +
+ +.larger[ +Data collection easy to standardize (BIDS, scanners' software) + +Statistical modeling keep analytical flexibility not to stifle the development of new ideas + +Preprocessing offers an **opportunity** to reduce analytical flexibility and **enable** cross-study comparisons +] + +] + + --- # Standardizing preprocessing: visual reports @@ -825,6 +867,25 @@ --- +# Building a community was important to *fMRIPrep* + +.boxed-content.large[ +.no-bullet[ +* Feedback & support: + * error & bug reports help development, + * feature requests help driving a roadmap, + * questions are the entry point to deliver support + * [ NeuroStars.org](https://neurostars.org) + +* Engage contributors (see [our guidelines](https://www.nipreps.org/community/CONTRIBUTING/)): + * documentation, assistance debugging, code patches, everything counts! + +* Reach out, increase user-base. +] +] + +--- + # Standardizing preprocessing: software versions .larger[