-
Notifications
You must be signed in to change notification settings - Fork 10
/
Copy path5steps.html
172 lines (160 loc) · 8.37 KB
/
5steps.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
<!DOCTYPE html>
<html lang="en">
<head>
<!-- Google tag (gtag.js) -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-WJRL86VLXW"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-WJRL86VLXW');
</script>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>5Steps - ReproNim</title>
<!-- CSS -->
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css">
<link rel="stylesheet" href="https://code.ionicframework.com/ionicons/1.5.2/css/ionicons.min.css">
<link rel="stylesheet" href="css/style.css">
<!-- font -->
<link href='https://fonts.googleapis.com/css?family=Nova+Square' rel='stylesheet'>
<link rel="stylesheet" href="font/font.css">
</head>
<body>
<div id="wrapper">
<section class="section-1">
<header class="site-header">
<div class="container">
<div class="row">
<div class="col-sm-4 col-xs-8">
<h1 class="logo"><a href="index.html">ReproNim</a></h1>
</div>
<div class="col-sm-8 col-xs-4">
<nav class="navbar pull-right" role="navigation">
<!-- Brand and toggle get grouped for better mobile display -->
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target="#bs-example-navbar-collapse-1">
<span class="ion-navicon"></span>
</button>
<!-- Collect the nav links, forms, and other content for toggling -->
<div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
<ul class="nav navbar-nav">
<li><a href="discover.html">Discover</a></li>
<li><a href="describe.html">Describe</a></li>
<li><a href="do.html">Do</a></li>
<li><a href="teach.html">Teach</a></li>
<li><a href="fellowship.html">Fellowship</a></li>
<li><a href="community.html">Community</a></li>
<li><a href="search.html">🔍</a></li>
</ul>
</div>
</nav>
</div>
</div> <!-- row -->
</div>
</header> <!-- site header -->
</section>
<section>
<div class="container">
<div class="row">
<div class="col-md-12">
This page under construction, beware...
<br>
See this <a href="https://docs.google.com/document/d/1i2DVI1b4fBJuLAjKRcjPE6oV8233POa2hVrwz4ve2Xo/edit">link</a> for a publically-commentable draft of the future page...
<h1 class="main-page-header">5 Steps to More Reproducible Neuroimaging Research</h1>
</div>
<div class="col-md-12">
<p>
Going whole-hog into completely reproducible neuroimaging is hard. But, there are lots of little things you can do today to increase the reproducibility of your current studies.
</p>
<table style="width:100%;background-color:#f6f945;font-size:30px">
<tr>
<td><b>Study Design</b></td>
<td style="text-align:right"><a href="http://repronim.org/5Steps/design">repronim.org/5Steps/design</a></td>
</tr>
</table>
<!-- <h2 style="background-color:#f6f945">Study Design</h2> -->
<p>
<ul type="square">
<li>Build data shareability into the consent process - see <a href="http://open-brain-consent.readthedocs.io">Open Brain Consent</a>, for example.
<li>Plan your study with a RoadMap - see, for example, <a href="http://brainverse.repronim.org">BrainVerse</a>.
<li>Pre-register your study - at, for example, <a href="http://osf.io">Open Science Framework</a>.
</ul>
</p>
<table style="width:100%;background-color:#3ffff5;font-size:30px">
<tr>
<td><b>Data Collection</b></td>
<td style="text-align:right"><a href="http://repronim.org/5Steps/acquisition">repronim.org/5Steps/acquisition</a></td>
</tr>
</table>
<!-- <h2 style="background-color:#3ffff5"></h2> -->
<!-- <h2 >URL</h2> -->
<p>
<ul type="square">
<li>Adopt <a href="https://www.incf.org/activities/standards-and-best-practices">standards-based</a> data representation from the get go.
<li>Use <a href="http://reproin.repronim.org">ReproIn</a> to automate conversion of your imaging data to <a href="http://bids.neuroimaging.io">BIDS</a>.
<li>Annotate your metadata (all experimental details) as you collect it - see, for example, <a href="http://brainverse.repronim.org">BrainVerse</a>.
<li>Use a version control system for all files (data, code, environments, etc.) - i.e. <a href="http://datalad.org">DataLad</a>.
</ul>
</p>
<table style="width:100%;background-color:#b498d1;font-size:30px">
<tr>
<td><b>Data Processing</b></td>
<td style="text-align:right"><a href="http://repronim.org/5Steps/processing">repronim.org/5Steps/processing</a></td>
</tr>
</table>
<!-- <h2 style="background-color:#b498d1">Data Processing</h2> -->
<p>
<ul type="square">
<li>Document your software and computational environment - for example <a href="https://github.com/kaczmarj/neurodocker">NeuroDocker</a> and <a href="http://reproman.repronim.org">ReproMan</a>.
<li>Use containerization/virtualization to encapsulate and share analysis workflow (<a href="http://docker.com">Docker</a>, <a href="https://www.sylabs.io/">Singularity</a>, <a href="https://www.virtualbox.org/">Virtual Machines</a>, etc.).
<li>Annotate your results - using NeuroImaging Data Model (<a href="http://nidm.nidash.org">NIDM</a>), for example.
</ul>
</p>
<table style="width:100%;background-color:#f3e0ff;font-size:30px">
<tr>
<td><b>Statistical Analysis</b></td>
<td style="text-align:right"><a href="http://repronim.org/5Steps/stats">repronim.org/5Steps/stats</a></td>
</tr>
</table>
<!-- <h2 style="background-color:#f3e0ff">Statistical Analysis</h2> -->
<p>
<ul type="square">
<li>Most studies are underpowered, combat this by sharing your data and reusing available data to enable creating larger data sets, thereby increasing study power. Understand:
<ul type="square">
<li>Effect size, confidence intervals, power, positive predictive value and significance testing - some training materials can be found <a href="http://www.reproducibleimaging.org/module-stats/">here</a>.
</ul>
</ul>
</p>
<table style="width:100%;background-color:#ffe09e;font-size:30px">
<tr>
<td><b>Publication</b></td>
<td style="text-align:right"><a href="http://repronim.org/5Steps/publication">repronim.org/5Steps/publication</a></td>
</tr>
</table>
<!-- <h2 style="background-color:#ffe09e">Publication Content</h2> -->
<p>
<ul type="square">
<li>Include the anonymized raw data and workflow used - using resources such as <a href="https://zenodo.org/">zenodo</a>, etc.
<li>Include complete processed results
<li>Make it Findable, Accessible, Interoperable and Reusable (<a href="https://www.go-fair.org/fair-principles/">FAIR</a>)
</ul>
</p>
</div>
</div><!-- row -->
</div>
</section>
<footer class="site-footer">
<div>
<ul class="list-inline quicklinks">
<li>Copyright © ReproNim 2016-2024</div>
<li>Support: <a href="https://projectreporter.nih.gov/project_info_description.cfm?aid=8999833">NIH-NIBIB P41 EB019936</a></li>
<li>Site theme: themewagon.com</li>
</ul>
</div>
</footer>
</div> <!-- wrapper -->
<!-- js -->
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.2.0/js/bootstrap.min.js"></script>
</body>
</html>