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fix: style, html headers and update slide with BIDS tree of the dataset
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‎docs/assets/fmriprep-bootcamp-geneva2024/day1-02-bids/index.html

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<head>
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<title>fMRIPrep Bootcamp | Day 1 :: Brain Imaging Data Structure</title>
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<meta charset="utf-8">
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<link rel="stylesheet" type="text/css" href="/talks/assets/asciinema-player/asciinema-player.css" />
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<link rel="stylesheet" type="text/css" href="/assets/asciinema-player/asciinema-player.css" />
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<style>
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@import url(https://fonts.googleapis.com/css?family=Roboto+Mono:400,700,400italic);
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transform: translateY(-50%);
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}
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.remark-slide-content { height: 100%; padding: 0; }
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.remark-slide-content h1 { font-size: 3em; }
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.remark-slide-content h2 { font-size: 2em; }
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.remark-slide-content h3 { font-size: 1.6em; }
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.remark-slide-content { height: 100%; padding: 0; font-size: 16pt;}
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.remark-slide-content h1 { font-size: 2em; color: #324989; }
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.remark-slide-content h2 { font-size: 1.5em; color: #324989; }
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.remark-slide-content h3 { font-size: 1.2em; color: #324989; }
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.footnote {
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position: absolute;
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bottom: 3em;
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font-size: 0.7em;
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left: 6em;
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}
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li p { line-height: 1.25em; }
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.remark-slide-content>p { margin-left: 60px; }
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.remark-slide-content>ul { margin-left: 60px; }
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.remark-slide-content>ul li { margin-left: 0.8em; }
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.no-bullet > ul {
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.no-bullet > ul > li > ul {
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padding-left: 2.8em;
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}
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.red { color: #fa0000; }
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.blue { color: #0000fa; }
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.green { color: #698b69; }
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.large { font-size: 2em; }
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a, a > code {
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color: rgb(249, 38, 114);
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text-decoration: none;
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.remark-code, .remark-inline-code { font-family: 'Roboto Mono'; }
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.large .remark-code, .large .remark-inline-code { font-size: 0.8em; }
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.remark-code-line-highlighted { background-color: #373832; }
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width: 45%;
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width: 80%;
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}
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em {
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strong {
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color: #324989;
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.gray-text {
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color: #888;
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.gray-text em, .gray-text strong {
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color: #888;
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.perma-sidebar {
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background-color: #324989;
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left: 20px;
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}
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#slide-how .slides {
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font-size: 0.9em;
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/*font-size: .9em;*/
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right: 140px;
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color: #000;
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width: 50%;
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margin-right: 2.5em;
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/* Two-column layout (60% left) */
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.left-column3 {
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}
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.small {
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font-size: 12pt;
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font-size: 0.7em;
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.larger {
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.large {
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.boxed-content {
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display: block;
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width: 89%;
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clear: both;
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/*
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.distribute {
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color: transparent; /* make the text invisible */
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user-select: none; /* prevent selection of the text */
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}
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.gray-text {
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.install-cmd {
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position: absolute;
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figure {
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margin-left: auto;
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font-size: 8pt;
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figcaption {
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text-decoration: underline dotted;
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</style>
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</head>
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<body>
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<script src="/talks/assets/asciinema-player/asciinema-player.min.js"></script>
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<script src="/assets/asciinema-player/asciinema-player.min.js"></script>
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<script src="https://kit.fontawesome.com/7e31cfd31d.js" crossorigin="anonymous"></script>
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<script type="text/javascript"
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src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS_CHTML">
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## The Brain Imaging Data Structure (BIDS)
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#### Chris Markiewicz &lt;<code>[email protected]</code>> & Oscar Esteban &lt;<code>[email protected]</code>>
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Chris Markiewicz &lt;<code>[email protected]</code>>
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Oscar Esteban &lt;<code>[email protected]</code>>
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]
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---
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## Outlook
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# Outlook
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.right-column3.center[
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<a href="https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/day1-02-bids/">
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.large[
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<br />
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* Overview of the neuroimaging pipeline structure
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* Why do data require preprocessing?
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* *fMRIPrep*
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* [Hi]story behind the tool
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* Why — just preprocessing
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* Why — standardization
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* Why — community
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* *NiPreps*
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*
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]]
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template: newsection
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name: BIDS
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# BIDS: Brain Imaging Data Structure
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---
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layout: true
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template: BIDS
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.pull-left[![Bids Layout](images/bids.png)]
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---
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# BIDS: Brain Imaging Data Structure
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.pull-right[
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<i class="fa-solid fa-folder-open"></i> my_dataset/<br />
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* BIDS is a directory structure, based on common practices
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* Builds on existing standards (NIfTI, JSON, TSV)
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---
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# BIDS: Brain Imaging Data Structure
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<i class="fa-solid fa-folder-open"></i> my_dataset/<br />
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* Basic metadata in the file names
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* Subject, session, imaging modality, etc.
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* Generally just enough to assign unique names
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]
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---
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count: false
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.pull-right[
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* Basic metadata in the file names
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* Subject, session, imaging modality, etc.
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* Generally just enough to assign unique names
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--
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.right-column2[
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image-related metadata
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---
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.pull-right[
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* Subject, session, imaging modality, etc.
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* Generally just enough to assign unique names
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* NIfTI headers and JSON sidecars contain detailed,
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image-related metadata
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--
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.right-column2[
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* [`dataset_description.json`](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#dataset_descriptionjson),
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[`participants.tsv`](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#participants-file),
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[`sessions.tsv`](https://bids-specification.readthedocs.io/en/stable/05-longitudinal-and-multi-site-studies.html#sessions-file),

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