-
Notifications
You must be signed in to change notification settings - Fork 7
/
Copy pathmkdocs.yml
272 lines (263 loc) · 13.5 KB
/
mkdocs.yml
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
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
# Project information
site_name: SPM Documentation
site_url: https://www.fil.ion.ucl.ac.uk/spm/docs/
site_author: SPM Team
site_description: >-
Documentation of the SPM Software for neuroimaging
# Repository
repo_url: https://github.com/spm/spm
repo_name: spm/spm
edit_uri: https://github.com/spm/spm-docs/blob/main/docs/
# Copyright
copyright: Copyright © 1991 - 2024 SPM Team and Collaborators
# Configuration
theme:
name: material
palette:
- media: "(prefers-color-scheme)"
primary: blue grey
accent: deep orange
toggle:
icon: material/brightness-auto
name: Switch to light mode
- media: "(prefers-color-scheme: light)"
scheme: default
primary: blue grey
accent: deep orange
toggle:
icon: material/brightness-7
name: Switch to dark mode
- media: "(prefers-color-scheme: dark)"
scheme: slate
primary: blue grey
accent: deep orange
toggle:
icon: material/brightness-4
name: Switch to system preference
logo: assets/images/spm_logo_white.png
favicon: assets/images/spm_favicon.png
icon:
repo: fontawesome/brands/github
features:
- content.code.copy
- content.tabs.link
- content.tooltips
- content.action.edit
- navigation.footer
- navigation.indexes
- navigation.sections
- navigation.tabs
- navigation.tabs.sticky
- navigation.top
nav:
- 'Home':
- 'index.md'
- 'Installation': 'installation/index.md'
- 'Courses': 'courses/index.md'
- 'Tutorials': 'tutorials/index.md'
- 'Development': 'development/index.md'
- 'Getting started':
- 'installation/index.md'
- 'Installation': 'installation/index.md'
- 'Standalone': 'installation/standalone.md'
- 'Containers': 'installation/containers.md'
- 'Octave': 'installation/octave.md'
- 'Tutorials':
- 'tutorials/index.md'
- 'fMRI':
- 'tutorials/fmri/index.md'
- 'Block design fMRI':
- 'Getting started': 'tutorials/fmri/block/index.md'
- 'Preprocessing':
- 'Introduction': 'tutorials/fmri/block/preprocessing/introduction.md'
- 'Visual inspection': 'tutorials/fmri/block/preprocessing/visual_inspection.md'
- 'Removal of dummy scans': 'tutorials/fmri/block/preprocessing/dummy_scans.md'
- 'Realignment': 'tutorials/fmri/block/preprocessing/realignment.md'
- 'Slice timing correction': 'tutorials/fmri/block/preprocessing/slice_timing.md'
- 'Coregistration': 'tutorials/fmri/block/preprocessing/coregistration.md'
- 'Segmentation': 'tutorials/fmri/block/preprocessing/segmentation.md'
- 'Normalisation': 'tutorials/fmri/block/preprocessing/normalisation.md'
- 'Smoothing': 'tutorials/fmri/block/preprocessing/smoothing.md'
- 'Batch interface': 'tutorials/fmri/block/preprocessing/batch.md'
- 'Scripting': 'tutorials/fmri/block/preprocessing/scripting.md'
- 'Statistical modelling':
- 'First-level modelling - block design': 'tutorials/fmri/block/modelling/block_design.md'
- 'Event-related fMRI':
- 'Getting started': 'tutorials/fmri/event/index.md'
- 'Preprocessing': 'tutorials/fmri/event/preprocessing.md'
- 'Categorical Modelling': 'tutorials/fmri/event/categorical.md'
- 'Parametric Modelling': 'tutorials/fmri/event/parametric.md'
- 'Bayesian Analysis': 'tutorials/fmri/event/bayesian.md'
- 'Group-level fMRI':
- 'Getting started': 'tutorials/fmri/group/index.md'
- 'One-sample t-test': 'tutorials/fmri/group/one_sample_ttest.md'
- 'Two-sample t-test': 'tutorials/fmri/group/two_sample_ttest.md'
- 'Factorial': 'tutorials/fmri/group/factorial.md'
- 'VBM':
- 'Getting started': 'tutorials/vbmcourse24/index.md'
#- 'Data preparation': 'tutorials/vbmcourse24/data_prep.md'
- 'Preprocessing': 'tutorials/vbmcourse24/preprocessing.md'
- 'Analysis': 'tutorials/vbmcourse24/analysis.md'
#- 'Getting started': 'tutorials/vbm/index.md'
#- 'Image processing': 'tutorials/vbm/image_processing.md'
#- 'Statistical analysis': 'tutorials/vbm/statistical_analysis.md'
- 'M/EEG':
- 'Getting started': 'tutorials/MEEG/index.md'
- 'EEG mismatch negativity data': 'tutorials/MEEG/mmn/index.md'
- 'Advanced topics in artefact removal': 'tutorials/MEEG/artefact.md'
- 'M/EEG convolution modelling': 'tutorials/MEEG/meeg_firstlevel.md'
- 'MEG source localisation': 'tutorials/MEEG/meg_sloc.md'
- 'Multimodal':
- 'Introduction': 'tutorials/MEEG/multimodal/index.md'
- 'EEG': 'tutorials/MEEG/multimodal/eeg.md'
- 'MEG': 'tutorials/MEEG/multimodal/meg.md'
- 'fMRI': 'tutorials/MEEG/multimodal/fmri.md'
- 'Fusion': 'tutorials/MEEG/multimodal/fusion.md'
- 'Multimodal, multisubject data fusion':
- 'Overview': 'tutorials/MEEG/multi/index.md'
- 'Preprocessing': 'tutorials/MEEG/multi/preprocessing.md'
- 'Evoked analysis': 'tutorials/MEEG/multi/evoked.md'
- 'Time-frequency analysis': 'tutorials/MEEG/multi/timefrequency.md'
- 'fMRI': 'tutorials/MEEG/multi/fmri.md'
- 'Source': 'tutorials/MEEG/multi/source.md'
- 'References': 'tutorials/MEEG/multi/references.md'
- 'OPM':
- 'Getting started': 'tutorials/opm/index.md'
- 'Sensor level: Evoked response': 'tutorials/opm/evoked/index.md'
- 'Source level: Evoked response': 'tutorials/opm/evoked_source/index.md'
- 'Coregistration': 'tutorials/opm/coreg/index.md'
- 'Simulation': 'tutorials/opm/simulation/index.md'
- 'Supported file formats': 'tutorials/opm/formats/index.md'
- 'DCM':
- 'Overview of DCM': 'tutorials/dcm/index.md'
- 'DCM for fMRI - 1st level (Attention)': 'tutorials/dcm/dcm_fmri_first_level_gui.md'
- 'DCM for fMRI - 2nd level (Motor)': 'tutorials/dcm/dcm_fmri_second_level_motor.md'
- 'DCM for fMRI - 1st level (Language)': 'tutorials/dcm/dcm_fmri_first_level.md'
- 'DCM for fMRI - 2nd level (Language)': 'tutorials/dcm/dcm_fmri_second_level.md'
- 'DCM for evoked responses': 'tutorials/dcm/dcm_erp.md'
- 'DCM for induced responses': 'tutorials/dcm/dcm_ir.md'
- 'DCM for phase coupling': 'tutorials/dcm/dcm_phase.md'
- 'DCM for steady state responses': 'tutorials/dcm/dcm_ssr.md'
- 'DCM for cross-spectral densities': 'tutorials/dcm/dcm_csd.md'
- 'DAiSS':
- 'Overview of DAiSS': 'tutorials/daiss/index.md'
- 'Beamforming: MEGIN/Elekta/Neuromag': 'tutorials/daiss/beamforming/neuromag/index.md'
- 'Beamforming: OPM': 'tutorials/daiss/beamforming/opm/index.md'
- 'Beamforming: Simulated Data': 'tutorials/daiss/beamforming/simulated/index.md'
- 'Courses':
- 'courses/index.md'
- 'M/EEG':
- 'courses/eeg_meg/index.md'
- 'Course schedule': 'courses/eeg_meg/programme.md'
- 'Datasets': 'courses/eeg_meg/eeg_datasets.md'
- 'Lecture recordings':
- 'Overview': 'courses/eeg_meg/recordings/index.md'
- 'Introduction & resources': 'courses/eeg_meg/recordings/introduction.md'
- 'What are we measuring with M/EEG?': 'courses/eeg_meg/recordings/what_measured.md'
- 'Data preprocessing (talk & demo)': 'courses/eeg_meg/recordings/preprocessing.md'
- 'General linear model (GLM) and classical inference': 'courses/eeg_meg/recordings/glm_classical_inference.md'
- 'Convolutional GLM': 'courses/eeg_meg/recordings/glm_convolutional.md'
- 'Multiple comparisons - problems & solutions': 'courses/eeg_meg/recordings/multiple_comparisons.md'
- 'Analysis of optically pumped magnetometer (OPM) data (talk & demo)': 'courses/eeg_meg/recordings/opm_analysis.md'
- 'Bayesian inference': 'courses/eeg_meg/recordings/bayesian_inference.md'
- 'M/EEG source analysis (talk & demo)': 'courses/eeg_meg/recordings/source_analysis.md'
- 'The principles of dynamic causal modelling (DCM)': 'courses/eeg_meg/recordings/dcm_principles.md'
- 'DCM for evoked responses': 'courses/eeg_meg/recordings/dcm_evoked_responses.md'
- 'DCM for cross-spectral densities (talk & DCM demo)': 'courses/eeg_meg/recordings/dcm_cross_spectral_desities.md'
- 'Bayesian model selection and averaging': 'courses/eeg_meg/recordings/bayesian_model_selection.md'
- 'DAiSS: An SPM toolbox for alternate source imaging approaches (talk & demo)': 'courses/eeg_meg/recordings/daiss.md'
- 'Group M/EEG data analysis': 'courses/eeg_meg/recordings/group_analysis.md'
- 'fMRI/VBM':
- 'courses/fmri_vbm/index.md'
- 'Course schedule': 'courses/fmri_vbm/programme.md'
- 'Datasets': 'courses/fmri_vbm/mri_datasets.md'
- 'Preparatory materials': 'courses/fmri_vbm/preparatory_materials.md'
- 'Learning objectives': 'courses/fmri_vbm/learning_objectives.md'
- 'Lecture recordings':
- 'Overview': 'courses/fmri_vbm/recordings/index.md'
- 'Spatial preprocessing': 'courses/fmri_vbm/recordings/preprocessing.md'
- 'General linear model': 'courses/fmri_vbm/recordings/glm.md'
- 'Contrasts & classical inference': 'courses/fmri_vbm/recordings/contrasts_classical_inference.md'
- 'Group analysis': 'courses/fmri_vbm/recordings/group_analysis.md'
- 'Random field theory': 'courses/fmri_vbm/recordings/random_field_theory.md'
- 'Voxel-based morphometry': 'courses/fmri_vbm/recordings/vbm.md'
- 'Experimental design': 'courses/fmri_vbm/recordings/experimental_design.md'
- 'Event-related fMRI': 'courses/fmri_vbm/recordings/event_related_fmri.md'
- 'Bayesian inference': 'courses/fmri_vbm/recordings/bayesian_inference.md'
- 'Introduction to DCM': 'courses/fmri_vbm/recordings/dcm_introduction.md'
- 'DCM: Testing hypotheses': 'courses/fmri_vbm/recordings/dcm_hypothesis_testing.md'
- 'Earlier recordings': 'courses/fmri_vbm/recordings/fmri_legacy_recordings.md'
- 'Reference documentation':
- 'reference/index.md'
- 'M/EEG':
- 'Getting started': 'reference/MEEG/index.md'
- 'M/EEG preprocessing': 'reference/MEEG/eeg_preprocessing.md'
- 'Sensor-level analysis': 'reference/MEEG/eeg_sensoranalysis.md'
- 'Source imaging': 'reference/MEEG/eeg_imaging.md'
- 'DCM for evoked responses': 'reference/MEEG/eeg_DCM.md'
- 'Development':
- 'Introduction': 'development/index.md'
- 'Git': 'development/git.md'
- 'Guidelines': 'development/guidelines.md'
- 'Testing': 'development/testing.md'
- 'Compilation': 'development/compilation/index.md'
- 'Versioning': 'development/versioning.md'
markdown_extensions:
- abbr
- admonition
- attr_list
- def_list
- footnotes
- meta
- md_in_html
#- mdx_truly_sane_lists
- pymdownx.arithmatex:
generic: true
- pymdownx.caret
- pymdownx.details
- pymdownx.emoji:
emoji_index: !!python/name:materialx.emoji.twemoji
emoji_generator: !!python/name:materialx.emoji.to_svg
- pymdownx.highlight:
anchor_linenums: true
- pymdownx.inlinehilite
- pymdownx.keys
- pymdownx.mark
- pymdownx.snippets
- pymdownx.superfences
- pymdownx.tabbed:
alternate_style: true
slugify: !!python/object/apply:pymdownx.slugs.slugify
kwds:
case: lower
- pymdownx.tasklist:
custom_checkbox: true
- pymdownx.tilde
- smarty
- tables
- toc:
permalink: true
plugins:
- mkdocs-video:
css_style:
width: "100%"
height: "42.172vw"
is_video: True
video_autoplay: False
- bibtex:
bib_file: "docs/assets/bib/spm.bib"
- search:
lang: en
extra:
generator: false
social:
- icon: fontawesome/brands/github
link: https://github.com/spm
- icon: fontawesome/solid/brain
link: https://www.fil.ion.ucl.ac.uk/spm/
extra_css:
- assets/css/extra.css
extra_javascript:
- assets/javascripts/mathjax.js
- https://polyfill.io/v3/polyfill.min.js?features=es6
- https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js