Wiki source code of Brainstorm

Version 60.1 by abonard on 2025/04/10 15:05
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adavison 1.1 1
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abonard 3.1 3 * ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
jessicamitchell 2.1 4
abonard 8.1 5 * ((( ==== **[[Intermediate >>||anchor = "HIntermediate-1"]]** ==== )))
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abonard 12.1 7 * ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
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abonard 3.1 9 === **Beginner** ===
jessicamitchell 2.1 10
abonard 3.1 11 === [[Starting a new study – Explore the anatomy>>https://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy||rel=" noopener noreferrer" target="_blank"]] ===
jessicamitchell 2.1 12
abonard 3.1 13 **Level**: beginner(%%) **Type**: interactive tutorial
jessicamitchell 2.1 14
abonard 3.1 15 By attending this tutorial, learners will know to how to create a new subject, how to import the anatomy, how we can best use the MRI Viewer, what are fiducial points and how can we use them, how does the validation work and how to get MNI coordinates.
abonard 4.1 16 === [[Starting a new study – Create a new protocol>>https://neuroimage.usc.edu/brainstorm/Tutorials/CreateProtocol||rel=" noopener noreferrer" target="_blank"]] ===
jessicamitchell 2.1 17
abonard 4.1 18 **Level**: beginner(%%) **Type**: interactive tutorial
19
20 If you are a complete beginner and new to Brainstorms start with this tutorial!
21 We will guide you through your first set up of the Brainstorm interface, the Database structure and files, how to create your first protocol and how to further explore your protocol and finally show you how you can set up a backup and how to change temporary folders.
abonard 5.1 22 === [[Brainstorm: Imaging neural activity at the speed of brain>>https://www.youtube.com/watch?v=30eFJUrRcN4||rel=" noopener noreferrer" target="_blank"]] ===
abonard 4.1 23
abonard 5.1 24 **Level**: beginner(%%) **Type**: video tutorial
25
26 In this tutorial we will first give you a basic introduction into the objectives and basic principles of Brainstorms. In the following short demo you will get an insight into the database and processing, we will show you how to use notch filters and QC and how to import data into your project. You will further see how the source imaging works and how to use the time frequency decomposition.
27 {{html}}
28 <iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/30eFJUrRcN4" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
29 {{/html}}
abonard 6.1 30 === [[Starting a new study – Import the subject anatomy>>https://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 5.1 31
abonard 6.1 32 **Level**: beginner(%%) **Type**: interactive tutorial
33
34 Picking up were we left off in the previous tutorial, we will now look into how to create a new subject, how to import the anatomy, how we can best use the MRI Viewer, what are fiducial points and how can we use them, how does the validation work and how to get MNI coordinates.
abonard 7.1 35 === [[Introduction tutorials>>https://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction||rel=" noopener noreferrer" target="_blank"]] ===
abonard 6.1 36
abonard 7.1 37 **Level**: beginner(%%) **Type**: -
38
abonard 8.1 39 === **Intermediate** ===
abonard 7.1 40
abonard 8.1 41 === [[Reviewing – Event markers>>https://neuroimage.usc.edu/brainstorm/Tutorials/EventMarkers||rel=" noopener noreferrer" target="_blank"]] ===
42
43 **Level**: intermediate(%%) **Type**: interactive tutorial
44
abonard 9.1 45 === [[Reviewing – Continuous recordings>>https://neuroimage.usc.edu/brainstorm/Tutorials/ReviewRaw||rel=" noopener noreferrer" target="_blank"]] ===
abonard 8.1 46
abonard 9.1 47 **Level**: intermediate(%%) **Type**: interactive tutorial
48
abonard 10.1 49 === [[Reviewing – Multiple windows>>https://neuroimage.usc.edu/brainstorm/Tutorials/MultipleWindows||rel=" noopener noreferrer" target="_blank"]] ===
abonard 9.1 50
abonard 10.1 51 **Level**: intermediate(%%) **Type**: interactive tutorial
52
abonard 11.1 53 === [[Reviewing – Channel file / MRI registration>>https://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile||rel=" noopener noreferrer" target="_blank"]] ===
abonard 10.1 54
abonard 11.1 55 **Level**: intermediate(%%) **Type**: interactive tutorial
56
abonard 12.1 57 === **Advanced** ===
abonard 11.1 58
abonard 12.1 59 === [[Export surface source maps to SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm12||rel=" noopener noreferrer" target="_blank"]] ===
60
61 **Level**: advanced(%%) **Type**: -
62
abonard 13.1 63 === [[MEG current phantom (Elekta-Neuromag)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomElekta||rel=" noopener noreferrer" target="_blank"]] ===
abonard 12.1 64
abonard 13.1 65 **Level**: advanced(%%) **Type**: -
66
abonard 14.1 67 === [[Plugins>>https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins||rel=" noopener noreferrer" target="_blank"]] ===
abonard 13.1 68
abonard 14.1 69 **Level**: advanced(%%) **Type**: -
70
abonard 15.1 71 === [[FEM mesh generation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMesh||rel=" noopener noreferrer" target="_blank"]] ===
abonard 14.1 72
abonard 15.1 73 **Level**: advanced(%%) **Type**: -
74
abonard 16.1 75 === [[Group analysis: Subject coregistration>>https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects||rel=" noopener noreferrer" target="_blank"]] ===
abonard 15.1 76
abonard 16.1 77 **Level**: advanced(%%) **Type**: -
78
abonard 17.1 79 === [[FEM advanced tutorial with MEG/EEG Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMedianNerve||rel=" noopener noreferrer" target="_blank"]] ===
abonard 16.1 80
abonard 17.1 81 **Level**: advanced(%%) **Type**: -
82
abonard 18.1 83 === [[Connectivity>>https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity||rel=" noopener noreferrer" target="_blank"]] ===
abonard 17.1 84
abonard 18.1 85 **Level**: advanced(%%) **Type**: -
86
abonard 19.1 87 === [[Corticomuscular coherence (CTF MEG)>>https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence||rel=" noopener noreferrer" target="_blank"]] ===
abonard 18.1 88
abonard 19.1 89 **Level**: advanced(%%) **Type**: -
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abonard 20.1 91 === [[Best: Brain Entropy in space and time>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutBEst||rel=" noopener noreferrer" target="_blank"]] ===
abonard 19.1 92
abonard 20.1 93 **Level**: advanced(%%) **Type**: -
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abonard 21.1 95 === [[Epileptogenic Zone Fingerprint>>https://neuroimage.usc.edu/brainstorm/Tutorials/EZFingerprint||rel=" noopener noreferrer" target="_blank"]] ===
abonard 20.1 96
abonard 21.1 97 **Level**: advanced(%%) **Type**: -
98
abonard 22.1 99 === [[SSP Cookbook>>https://neuroimage.usc.edu/brainstorm/Tutorials/SSPCookbook||rel=" noopener noreferrer" target="_blank"]] ===
abonard 21.1 100
abonard 22.1 101 **Level**: advanced(%%) **Type**: -
102
abonard 23.1 103 === [[Elekta-Neuromag tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag||rel=" noopener noreferrer" target="_blank"]] ===
abonard 22.1 104
abonard 23.1 105 **Level**: advanced(%%) **Type**: -
106
abonard 24.1 107 === [[Using BrainVISA>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainVisa||rel=" noopener noreferrer" target="_blank"]] ===
abonard 23.1 108
abonard 24.1 109 **Level**: advanced(%%) **Type**: -
110
abonard 25.1 111 === [[MEG median nerve tutorial (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/MedianNerveCtf||rel=" noopener noreferrer" target="_blank"]] ===
abonard 24.1 112
abonard 25.1 113 **Level**: advanced(%%) **Type**: -
114
abonard 26.1 115 === [[Spike Sorting in Brainstorm>>https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting||rel=" noopener noreferrer" target="_blank"]] ===
abonard 25.1 116
abonard 26.1 117 **Level**: advanced(%%) **Type**: -
118
abonard 27.1 119 === [[Coordinate systems>>https://neuroimage.usc.edu/brainstorm/CoordinateSystems||rel=" noopener noreferrer" target="_blank"]] ===
abonard 26.1 120
abonard 27.1 121 **Level**: advanced(%%) **Type**: -
122
abonard 28.1 123 === [[Real-time head-tracking for adjusting head position>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime||rel=" noopener noreferrer" target="_blank"]] ===
abonard 27.1 124
abonard 28.1 125 **Level**: advanced(%%) **Type**: -
126
abonard 29.1 127 === [[Spectral Parameterization Resolved in Time (SPRiNT)>>https://neuroimage.usc.edu/brainstorm/Tutorials/SPRiNT||rel=" noopener noreferrer" target="_blank"]] ===
abonard 28.1 128
abonard 29.1 129 **Level**: advanced(%%) **Type**: -
130
abonard 30.1 131 === [[Montage editor>>https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor||rel=" noopener noreferrer" target="_blank"]] ===
abonard 29.1 132
abonard 30.1 133 **Level**: advanced(%%) **Type**: -
134
abonard 31.1 135 === [[Tutorial - Head Motion>>https://neuroimage.usc.edu/brainstorm/Tutorials/HeadMotion||rel=" noopener noreferrer" target="_blank"]] ===
abonard 30.1 136
abonard 31.1 137 **Level**: advanced(%%) **Type**: -
138
abonard 32.1 139 === [[Virtual Fiber Tracks for Connectivity Visualization>>https://neuroimage.usc.edu/brainstorm/Tutorials/FiberConnectivity||rel=" noopener noreferrer" target="_blank"]] ===
abonard 31.1 140
abonard 32.1 141 **Level**: advanced(%%) **Type**: -
142
abonard 33.1 143 === [[MEG visual tutorial: Single subject (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle||rel=" noopener noreferrer" target="_blank"]] ===
abonard 32.1 144
abonard 33.1 145 **Level**: advanced(%%) **Type**: -
146
abonard 34.1 147 === [[Digitize EEG sensor locations and head shape>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutDigitize||rel=" noopener noreferrer" target="_blank"]] ===
abonard 33.1 148
abonard 34.1 149 **Level**: advanced(%%) **Type**: -
150
abonard 35.1 151 === [[MEG visual tutorial: Group analysis (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup||rel=" noopener noreferrer" target="_blank"]] ===
abonard 34.1 152
abonard 35.1 153 **Level**: advanced(%%) **Type**: -
154
abonard 36.1 155 === [[Converting to Brainstorm Events>>https://neuroimage.usc.edu/brainstorm/e-phys/ConvertToBrainstormEvents||rel=" noopener noreferrer" target="_blank"]] ===
abonard 35.1 156
abonard 36.1 157 **Level**: advanced(%%) **Type**: -
158
abonard 37.1 159 === [[Synchronization with eye tracker (event transfer)>>https://neuroimage.usc.edu/brainstorm/Tutorials/EyetrackSynchro||rel=" noopener noreferrer" target="_blank"]] ===
abonard 36.1 160
abonard 37.1 161 **Level**: advanced(%%) **Type**: -
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abonard 38.1 163 === [[Using the anatomy templates>>https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 37.1 164
abonard 38.1 165 **Level**: advanced(%%) **Type**: -
166
abonard 39.1 167 === [[Fitting dipoles with FieldTrip>>https://neuroimage.usc.edu/brainstorm/Tutorials/DipoleFitting||rel=" noopener noreferrer" target="_blank"]] ===
abonard 38.1 168
abonard 39.1 169 **Level**: advanced(%%) **Type**: -
170
abonard 40.1 171 === [[Deriving LFP signals from raw signals>>https://neuroimage.usc.edu/brainstorm/e-phys/RawToLFP||rel=" noopener noreferrer" target="_blank"]] ===
abonard 39.1 172
abonard 40.1 173 **Level**: advanced(%%) **Type**: -
174
abonard 41.1 175 === [[MEG current phantom (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomCtf||rel=" noopener noreferrer" target="_blank"]] ===
abonard 40.1 176
abonard 41.1 177 **Level**: advanced(%%) **Type**: -
178
abonard 42.1 179 === [[Resting state recordings from the OMEGA database>>https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega||rel=" noopener noreferrer" target="_blank"]] ===
abonard 41.1 180
abonard 42.1 181 **Level**: advanced(%%) **Type**: -
182
abonard 43.1 183 === [[Realistic head model: FEM with DUNEuro>>https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro||rel=" noopener noreferrer" target="_blank"]] ===
abonard 42.1 184
abonard 43.1 185 **Level**: advanced(%%) **Type**: -
186
abonard 44.1 187 === [[Functions for Basic e-phys>>https://neuroimage.usc.edu/brainstorm/e-phys/functions||rel=" noopener noreferrer" target="_blank"]] ===
abonard 43.1 188
abonard 44.1 189 **Level**: advanced(%%) **Type**: -
190
abonard 45.1 191 === [[MRI segmentation with FastSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegFastSurfer||rel=" noopener noreferrer" target="_blank"]] ===
abonard 44.1 192
abonard 45.1 193 **Level**: advanced(%%) **Type**: -
194
abonard 46.1 195 === [[ECoG/sEEG tutorial>>https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG||rel=" noopener noreferrer" target="_blank"]] ===
abonard 45.1 196
abonard 46.1 197 **Level**: advanced(%%) **Type**: -
198
abonard 47.1 199 === [[Using FreeSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer||rel=" noopener noreferrer" target="_blank"]] ===
abonard 46.1 200
abonard 47.1 201 **Level**: advanced(%%) **Type**: -
202
abonard 48.1 203 === [[Granger causality>>https://neuroimage.usc.edu/brainstorm/GrangerCausality||rel=" noopener noreferrer" target="_blank"]] ===
abonard 47.1 204
abonard 48.1 205 **Level**: advanced(%%) **Type**: -
206
abonard 49.1 207 === [[EEG and epilepsy>>https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 48.1 208
abonard 49.1 209 **Level**: advanced(%%) **Type**: -
210
abonard 50.1 211 === [[Yokogawa/KIT tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/Yokogawa||rel=" noopener noreferrer" target="_blank"]] ===
abonard 49.1 212
abonard 50.1 213 **Level**: advanced(%%) **Type**: -
214
abonard 51.1 215 === [[MRI segmentation with CIVET>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCIVET||rel=" noopener noreferrer" target="_blank"]] ===
abonard 50.1 216
abonard 51.1 217 **Level**: advanced(%%) **Type**: -
218
abonard 52.1 219 === [[Fitting Oscillations and One-Over-F (FOOOF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/Fooof||rel=" noopener noreferrer" target="_blank"]] ===
abonard 51.1 220
abonard 52.1 221 **Level**: advanced(%%) **Type**: -
222
abonard 53.1 223 === [[Human Connectome Project: Resting-state MEG>>https://neuroimage.usc.edu/brainstorm/Tutorials/HCP-MEG||rel=" noopener noreferrer" target="_blank"]] ===
abonard 52.1 224
abonard 53.1 225 **Level**: advanced(%%) **Type**: -
226
abonard 54.1 227 === [[T1-MRI Segmentation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite||rel=" noopener noreferrer" target="_blank"]] ===
abonard 53.1 228
abonard 54.1 229 **Level**: advanced(%%) **Type**: -
230
abonard 55.1 231 === [[Connectivity Graphs>>https://neuroimage.usc.edu/brainstorm/Tutorials/ConnectivityGraph||rel=" noopener noreferrer" target="_blank"]] ===
abonard 54.1 232
abonard 55.1 233 **Level**: advanced(%%) **Type**: -
234
abonard 56.1 235 === [[Export raw files in BIDS format>>https://neuroimage.usc.edu/brainstorm/ExportBids||rel=" noopener noreferrer" target="_blank"]] ===
abonard 55.1 236
abonard 56.1 237 **Level**: advanced(%%) **Type**: -
238
abonard 57.1 239 === [[How to write your own process>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutUserProcess||rel=" noopener noreferrer" target="_blank"]] ===
abonard 56.1 240
abonard 57.1 241 **Level**: advanced(%%) **Type**: -
242
abonard 58.1 243 === [[FEM tensors estimation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemTensors||rel=" noopener noreferrer" target="_blank"]] ===
abonard 57.1 244
abonard 58.1 245 **Level**: advanced(%%) **Type**: -
246
abonard 59.1 247 === [[MRI Segmentation with CAT12>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12||rel=" noopener noreferrer" target="_blank"]] ===
abonard 58.1 248
abonard 59.1 249 **Level**: advanced(%%) **Type**: -
250
abonard 60.1 251 === [[Export volume source maps to SPM8 / SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm8||rel=" noopener noreferrer" target="_blank"]] ===
abonard 59.1 252
abonard 60.1 253 **Level**: advanced(%%) **Type**: -
254
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