Add docs.

.gitignore

@@ -1,5 +1,9 @@
-_site/
-Gemfile*
+Gemfile.lock
+_site
+.sass-cache
+.jekyll-cache
+.jekyll-metadata
+vendor
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

404.html

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+---
+permalink: /404.html
+layout: default
+---
+
+<style type="text/css" media="screen">
+  .container {
+    margin: 10px auto;
+    max-width: 600px;
+    text-align: center;
+  }
+  h1 {
+    margin: 30px 0;
+    font-size: 4em;
+    line-height: 1;
+    letter-spacing: -1px;
+  }
+</style>
+
+<div class="container">
+  <h1>404</h1>
+
+  <p><strong>Page not found :(</strong></p>
+  <p>The requested page could not be found.</p>
+</div>

Gemfile

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+source "https://rubygems.org"
+# Hello! This is where you manage which Jekyll version is used to run.
+# When you want to use a different version, change it below, save the
+# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
+#
+#     bundle exec jekyll serve
+#
+# This will help ensure the proper Jekyll version is running.
+# Happy Jekylling!
+# gem "jekyll", "~> 4.3.3"
+# This is the default theme for new Jekyll sites. You may change this to anything you like.
+gem "minima", "~> 2.5"
+# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
+# uncomment the line below. To upgrade, run `bundle update github-pages`.
+gem "github-pages", "~> 231", group: :jekyll_plugins
+# If you have any plugins, put them here!
+group :jekyll_plugins do
+  gem "jekyll-feed", "~> 0.12"
+end
+
+# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
+# and associated library.
+platforms :mingw, :x64_mingw, :mswin, :jruby do
+  gem "tzinfo", ">= 1", "< 3"
+  gem "tzinfo-data"
+end
+
+# Performance-booster for watching directories on Windows
+gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin]
+
+# Lock `http_parser.rb` gem to `v0.6.x` on JRuby builds since newer versions of the gem
+# do not have a Java counterpart.
+gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby]

README.md

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 # open-physio-data
-Open fMRI datasets with concurrent physio data. Focused on physio measures that correlate with autonomic state.
+
+Open fMRI datasets with concurrent physio data.
+Focused on physio measures that correlate with autonomic state.

_config.yml

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+# Welcome to Jekyll!
+#
+# This config file is meant for settings that affect your whole blog, values
+# which you are expected to set up once and rarely edit after that. If you find
+# yourself editing this file very often, consider using Jekyll's data files
+# feature for the data you need to update frequently.
+#
+# For technical reasons, this file is *NOT* reloaded automatically when you use
+# 'bundle exec jekyll serve'. If you change this file, please restart the server process.
+#
+# If you need help with YAML syntax, here are some quick references for you:
+# https://learn-the-web.algonquindesign.ca/topics/markdown-yaml-cheat-sheet/#yaml
+# https://learnxinyminutes.com/docs/yaml/
+#
+# Site settings
+# These are used to personalize your new site. If you look in the HTML files,
+# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
+# You can create any custom variable you would like, and they will be accessible
+# in the templates via {{ site.myvariable }}.
+
+title: Open Multi-Echo Datasets
+description: >-
+  A summary of available open multi-echo fMRI datasets
+baseurl: "/open-multi-echo-data" # the subpath of your site, e.g. /blog
+url: "https://me-ica.github.io" # the base hostname & protocol for your site, e.g. http://example.com
+
+# Build settings
+remote_theme: pages-themes/[email protected]
+plugins:
+- jekyll-remote-theme # add this line to the plugins list if you already have one
+
+# Exclude from processing.
+# The following items will not be processed, by default.
+# Any item listed under the `exclude:` key here will be automatically added to
+# the internal "default list".
+#
+# Excluded items can be processed by explicitly listing the directories or
+# their entries' file path in the `include:` list.
+#
+# exclude:
+#   - .sass-cache/
+#   - .jekyll-cache/
+#   - gemfiles/
+#   - Gemfile
+#   - Gemfile.lock
+#   - node_modules/
+#   - vendor/bundle/
+#   - vendor/cache/
+#   - vendor/gems/
+#   - vendor/ruby/

_layouts/dataset.html

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+---
+layout: default
+---
+
+<h1>{{ page.title }}</h1>
+
+<table>
+    <thead>
+        <tr>
+            <th>Magnetic Field Strength</th>
+            <th>Number(s) of Echoes</th>
+            <th>Extras</th>
+        </tr>
+    </thead>
+    <tbody>
+        <tr>
+            <td>{{ page.scanner }}</td>
+            <td>{{ page.echoes | join: ", " }}</td>
+            <td>
+                <ul>
+                    {% for extra in page.extras %}
+                        <li>
+                            {% if extra == "asl" %}
+                                Concurrent ASL
+                            {% elsif extra == "complex" %}
+                                Complex-valued BOLD
+                            {% elsif extra == "norf" %}
+                                Noise scans
+                            {% elsif extra == "physio" %}
+                                Concurrent physiological monitoring
+                            {% elsif extra == "single-echo" %}
+                                Comparison single-echo BOLD
+                            {% endif %}
+                        </li>
+                    {% endfor %}
+                </ul>
+            </td>
+        </tr>
+    </tbody>
+</table>
+
+<strong>
+<p>Raw Dataset: <a href="{{ page.website }}">{{ page.website }}</a></p>
+{% if page.fmriprep %}
+    <p>fMRIPrep derivatives: <a href="{{ page.fmriprep }}">{{ page.fmriprep }}</a></p>
+{% endif %}
+{% if page.afni %}
+    <p>AFNI derivatives: <a href="{{ page.afni }}">{{ page.afni }}</a></p>
+{% endif %}
+</strong>
+
+<hr/>
+
+{{content}}

_posts/2024-08-01-ds002278.md

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+---
+layout: dataset
+title: "Dense Investigation of Variability of Affect (DIVA)"
+categories: dataset
+website: https://openneuro.org/datasets/ds002278
+scanner: 3T
+physio: [ecg, eda, respiration]
+extras: [complex, multi-echo]
+---

_posts/template.md

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+---
+layout: dataset
+title: ""
+categories: dataset
+website:
+scanner:
+physio: []
+extras: []
+---

about.md

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+---
+layout: page
+title: About
+permalink: /about/
+---
+
+This is the base Jekyll theme. You can find out more info about customizing your Jekyll theme, as well as basic Jekyll usage documentation at [jekyllrb.com](https://jekyllrb.com/)
+
+You can find the source code for Minima at GitHub:
+[jekyll][jekyll-organization] /
+[minima](https://github.com/jekyll/minima)
+
+You can find the source code for Jekyll at GitHub:
+[jekyll][jekyll-organization] /
+[jekyll](https://github.com/jekyll/jekyll)
+
+
+[jekyll-organization]: https://github.com/jekyll

index.html

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+---
+# Feel free to add content and custom Front Matter to this file.
+# To modify the layout, see https://jekyllrb.com/docs/themes/#overriding-theme-defaults
+
+layout: home
+---
+
+<h1> {{ site.title }} </h1>
+
+This collects and describes every open fMRI dataset with concurrent physio data that we know of.
+
+We define "open" as being freely available to the public without registration or a data use agreement.
+This excludes several datasets that are fundamentally open,
+but which have barriers to access that would prevent researchers from directly downloading the data.
+
+<h2>Datasets</h2>
+
+{% assign physio = "" | split: "" %}
+{% assign extras = "" | split: "" %}
+{% for post in site.categories.dataset %}
+  {% assign physio = physio | concat: post.physio %}
+  {% assign extras = extras | concat: post.extras %}
+{% endfor %}
+{% assign physio = physio | uniq | sort %}
+{% assign extras = extras | uniq | sort %}
+
+<style>
+  table {
+    border-collapse: collapse;
+    width: 100%;
+  }
+  th, td {
+    border: 1px solid #ddd;
+    padding: 8px;
+  }
+  tr:nth-child(even) {
+    background-color: #f2f2f2;
+  }
+  tr:hover {
+    background-color: #ddd;
+  }
+  th {
+    padding-top: 12px;
+    padding-bottom: 12px;
+    text-align: left;
+    background-color: #4CAF50;
+    color: white;
+  }
+</style>
+
+<table>
+  <thead>
+    <tr>
+      <th style="max-width: 300px;">Title</th>
+      <th>URL</th>
+      <th>Scanner</th>
+      <th colspan="{{ physio.size }}">Physio Modalities</th>
+      <th colspan="{{ extras.size }}">Extra Features</th>
+    </tr>
+    <tr>
+      <th style="max-width: 300px;"></th>
+      <th></th>
+      <th></th>
+      {% for phys in physio %}
+        <th>{{ phys }}</th>
+      {% endfor %}
+      {% for extra in extras %}
+        <th>{{ extra }}</th>
+      {% endfor %}
+    </tr>
+  </thead>
+  <tbody>
+    {% for post in site.categories.dataset %}
+      <tr>
+        <td style="max-width: 300px;"><a href="{{ post.url | relative_url }}">{{ post.title }}</a></td>
+        <td style="text-align: center;"><a href="{{ post.website }}">Dataset</a></td>
+        <td style="text-align: center;">{{ post.scanner }}</td>
+        {% for phys in physio %}
+          <td style="text-align: center;">
+            {% if post.physio contains phys %}
+              X
+            {% endif %}
+          </td>
+        {% endfor %}
+        {% for extra in extras %}
+          <td style="text-align: center;">
+            {% if post.extras contains extra %}
+              X
+            {% endif %}
+          </td>
+        {% endfor %}
+      </tr>
+    {% endfor %}
+  </tbody>
+</table>