bids-specification/mkdocs.yml at master · bids-standard/bids-specification · GitHub

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
173
174
175
176
177
178
site_name: Brain Imaging Data Structure 1.11.2-dev
site_url: https://bids-specification.readthedocs.io/en/stable/
repo_url: https://github.com/bids-standard/bids-specification
nav:
  - The BIDS Specification:
      - Introduction: introduction.md
      - Common principles: common-principles.md
      - Modality agnostic files:
          - Dataset description: modality-agnostic-files/dataset-description.md
          - Data summary files: modality-agnostic-files/data-summary-files.md
          - Phenotypic and assessment data: modality-agnostic-files/phenotypic-and-assessment-data.md
          - Code: modality-agnostic-files/code.md
          - Events: modality-agnostic-files/events.md
      - Modality specific files:
          - Magnetic Resonance Imaging: modality-specific-files/magnetic-resonance-imaging-data.md
          - Magnetoencephalography: modality-specific-files/magnetoencephalography.md
          - Electroencephalography: modality-specific-files/electroencephalography.md
          - Intracranial Electroencephalography: modality-specific-files/intracranial-electroencephalography.md
          - Physiological recordings: modality-specific-files/physiological-recordings.md
          - Behavioral experiments (with no neural recordings): modality-specific-files/behavioral-experiments.md
          - Genetic Descriptor: modality-specific-files/genetic-descriptor.md
          - Positron Emission Tomography: modality-specific-files/positron-emission-tomography.md
          - Microscopy: modality-specific-files/microscopy.md
          - Near-Infrared Spectroscopy: modality-specific-files/near-infrared-spectroscopy.md
          - Motion: modality-specific-files/motion.md
          - Magnetic Resonance Spectroscopy: modality-specific-files/magnetic-resonance-spectroscopy.md
          - Electromyography: modality-specific-files/electromyography.md
      - Derivatives:
          - BIDS Derivatives: derivatives/introduction.md
          - Common data types and metadata: derivatives/common-data-types.md
          - Imaging data types: derivatives/imaging.md
          - Templates and atlases: derivatives/atlas.md
      - Longitudinal and multi-site studies: longitudinal-and-multi-site-studies.md
      - Glossary: glossary.md
      - BIDS Extension Proposals: extensions.md
      - Appendix:
          - Schema: appendices/schema.md
          - Contributors: appendices/contributors.md
          - Licenses: appendices/licenses.md
          - Entity table: appendices/entity-table.md
          - Entities: appendices/entities.md
          - File collections: appendices/file-collections.md
          - Units: appendices/units.md
          - Hierarchical Event Descriptors: appendices/hed.md
          - MEG file formats: appendices/meg-file-formats.md
          - MEG systems: appendices/meg-systems.md
          - Coordinate systems: appendices/coordinate-systems.md
          - Quantitative MRI: appendices/qmri.md
          - Arterial Spin Labeling: appendices/arterial-spin-labeling.md
          - Cross modality correspondence: appendices/cross-modality-correspondence.md
      - Changelog: CHANGES.md
  - The BIDS Website:
      - Getting started: https://bids.neuroimaging.io/getting_started/
      - Tutorials: https://bids.neuroimaging.io/getting_started/tutorials/
exclude_docs: |
  README.md
  pregh-changes.md
theme:
  name: material
  favicon: images/favicon.png
  logo: images/logo.png
  features:
    - navigation.sections
    - content.action.edit
  icon:
    repo: fontawesome/brands/github
    edit: material/pencil
  palette:
    # Palette toggle for automatic mode
    - media: (prefers-color-scheme)
      toggle:
        icon: material/brightness-auto
        name: Switch to light mode
      # Palette toggle for light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
      # Palette toggle for dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      toggle:
        icon: material/brightness-4
        name: Switch to system preference

edit_uri: https://github.com/bids-standard/bids-specification/edit/master/src/

copyright: Copyright &copy; BIDS Contributors - <a href="https://creativecommons.org/licenses/by/4.0/">CC BY 4.0</a>

extra:
  generator: false
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/bids-standard/bids-specification/
    - icon: fontawesome/brands/x-twitter
      link: https://x.com/BIDSstandard/
    - icon: fontawesome/brands/mastodon
      link: https://fosstodon.org/@bidsstandard
    - icon: fontawesome/brands/google
      link: https://groups.google.com/g/bids-discussion
    - icon: fontawesome/brands/instagram
      link: https://www.instagram.com/bidsstandard/
    - icon: fontawesome/brands/youtube
      link: https://www.youtube.com/channel/UCxZUcYfd_nvIVWAbzRB1tlw
  analytics:
    provider: google
    property: G-SBWH6YNMPX

extra_javascript:
  - js/jquery-3.6.0.min.js
extra_css:
  - css/tsv.css
  - css/dynamic-width.css
markdown_extensions:
  - toc:
      anchorlink: true
  - attr_list
  - pymdownx.superfences:
      preserve_tabs: true
      custom_fences:
        - name: tsv
          class: tsv
          format: !!python/name:bidsschematools.render.tsv.fence
        - name: tsvgz
          class: tsv
          format: !!python/name:bidsschematools.render.tsv.fence
  - admonition
  - pymdownx.details
plugins:
  - search
  - branchcustomization:
      update_config:
        - branch: /(?!^master$)/
          +extra_css:
            - css/watermark.css
  - macros:
      module_name: tools/mkdocs_macros_bids/main
      on_error_fail: true
  - redirects:
      redirect_maps:
        "01-introduction.md": "introduction.md"
        "02-common-principles.md": "common-principles.md"
        "03-modality-agnostic-files.md": "modality-agnostic-files/dataset-description.md"
        "modality-agnostic-files.md": "modality-agnostic-files/dataset-description.md"
        "04-modality-specific-files/01-magnetic-resonance-imaging-data.md": "modality-specific-files/magnetic-resonance-imaging-data.md"
        "04-modality-specific-files/02-magnetoencephalography.md": "modality-specific-files/magnetoencephalography.md"
        "04-modality-specific-files/03-electroencephalography.md": "modality-specific-files/electroencephalography.md"
        "04-modality-specific-files/04-intracranial-electroencephalography.md": "modality-specific-files/intracranial-electroencephalography.md"
        "04-modality-specific-files/05-task-events.md": "modality-agnostic-files/events.md"
        "04-modality-specific-files/06-physiological-and-other-continuous-recordings.md": "modality-specific-files/physiological-recordings.md"
        "04-modality-specific-files/07-behavioral-experiments.md": "modality-specific-files/behavioral-experiments.md"
        "04-modality-specific-files/08-genetic-descriptor.md": "modality-specific-files/genetic-descriptor.md"
        "04-modality-specific-files/09-positron-emission-tomography.md": "modality-specific-files/positron-emission-tomography.md"
        "04-modality-specific-files/10-microscopy.md": "modality-specific-files/microscopy.md"
        "04-modality-specific-files/11-near-infrared-spectroscopy.md": "modality-specific-files/near-infrared-spectroscopy.md"
        "05-derivatives/01-introduction.md": "derivatives/introduction.md"
        "05-derivatives/02-common-data-types.md": "derivatives/common-data-types.md"
        "05-derivatives/03-imaging.md": "derivatives/imaging.md"
        "06-longitudinal-and-multi-site-studies.md": "longitudinal-and-multi-site-studies.md"
        "07-extensions.md": "extensions.md"
        "99-appendices/14-glossary.md": "glossary.md"
        "99-appendices/01-contributors.md": "appendices/contributors.md"
        "99-appendices/02-licenses.md": "appendices/licenses.md"
        "99-appendices/03-hed.md": "appendices/hed.md"
        "99-appendices/04-entity-table.md": "appendices/entity-table.md"
        "99-appendices/05-units.md": "appendices/units.md"
        "99-appendices/06-meg-file-formats.md": "appendices/meg-file-formats.md"
        "99-appendices/07-meg-systems.md": "appendices/meg-systems.md"
        "99-appendices/08-coordinate-systems.md": "appendices/coordinate-systems.md"
        "99-appendices/09-entities.md": "appendices/entities.md"
        "99-appendices/10-file-collections.md": "appendices/file-collections.md"
        "99-appendices/11-qmri.md": "appendices/qmri.md"
        "99-appendices/12-arterial-spin-labeling.md": "appendices/arterial-spin-labeling.md"
        "99-appendices/13-cross-modality-correspondence.md": "appendices/cross-modality-correspondence.md"
        "modality-specific-files/task-events.md": "modality-agnostic-files/events.md"
docs_dir: "src"
use_directory_urls: false