Wiki source code of Brainstorm

Version 299.1 by abonard on 2025/06/13 16:08
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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 248.1 5 * ((( ==== **[[Intermediate >>||anchor = "HIntermediate-1"]]** ==== )))
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abonard 252.1 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 244.1 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 244.1 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 245.1 22 === [[Brainstorm: Imaging neural activity at the speed of brain>>https://www.youtube.com/watch?v=30eFJUrRcN4||rel=" noopener noreferrer" target="_blank"]] ===
abonard 244.1 23
abonard 245.1 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 246.1 30 === [[Starting a new study – Import the subject anatomy>>https://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 245.1 31
abonard 246.1 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 247.1 35 === [[Introduction tutorials>>https://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction||rel=" noopener noreferrer" target="_blank"]] ===
abonard 246.1 36
abonard 247.1 37 **Level**: beginner(%%) **Type**: -
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abonard 248.1 39 === **Intermediate** ===
abonard 247.1 40
abonard 248.1 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 249.1 45 === [[Reviewing – Continuous recordings>>https://neuroimage.usc.edu/brainstorm/Tutorials/ReviewRaw||rel=" noopener noreferrer" target="_blank"]] ===
abonard 248.1 46
abonard 249.1 47 **Level**: intermediate(%%) **Type**: interactive tutorial
48
abonard 250.1 49 === [[Reviewing – Multiple windows>>https://neuroimage.usc.edu/brainstorm/Tutorials/MultipleWindows||rel=" noopener noreferrer" target="_blank"]] ===
abonard 249.1 50
abonard 250.1 51 **Level**: intermediate(%%) **Type**: interactive tutorial
52
abonard 251.1 53 === [[Reviewing – Channel file / MRI registration>>https://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile||rel=" noopener noreferrer" target="_blank"]] ===
abonard 250.1 54
abonard 251.1 55 **Level**: intermediate(%%) **Type**: interactive tutorial
56
abonard 252.1 57 === **Advanced** ===
abonard 251.1 58
abonard 252.1 59 === [[Export surface source maps to SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm12||rel=" noopener noreferrer" target="_blank"]] ===
60
61 **Level**: advanced(%%) **Type**: -
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abonard 253.1 63 === [[MEG current phantom (Elekta-Neuromag)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomElekta||rel=" noopener noreferrer" target="_blank"]] ===
abonard 252.1 64
abonard 253.1 65 **Level**: advanced(%%) **Type**: -
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abonard 254.1 67 === [[Plugins>>https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins||rel=" noopener noreferrer" target="_blank"]] ===
abonard 253.1 68
abonard 254.1 69 **Level**: advanced(%%) **Type**: -
70
abonard 255.1 71 === [[FEM mesh generation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMesh||rel=" noopener noreferrer" target="_blank"]] ===
abonard 254.1 72
abonard 255.1 73 **Level**: advanced(%%) **Type**: -
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abonard 256.1 75 === [[Group analysis: Subject coregistration>>https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects||rel=" noopener noreferrer" target="_blank"]] ===
abonard 255.1 76
abonard 256.1 77 **Level**: advanced(%%) **Type**: -
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abonard 257.1 79 === [[FEM advanced tutorial with MEG/EEG Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMedianNerve||rel=" noopener noreferrer" target="_blank"]] ===
abonard 256.1 80
abonard 257.1 81 **Level**: advanced(%%) **Type**: -
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abonard 258.1 83 === [[Connectivity>>https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity||rel=" noopener noreferrer" target="_blank"]] ===
abonard 257.1 84
abonard 258.1 85 **Level**: advanced(%%) **Type**: -
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abonard 259.1 87 === [[Corticomuscular coherence (CTF MEG)>>https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence||rel=" noopener noreferrer" target="_blank"]] ===
abonard 258.1 88
abonard 259.1 89 **Level**: advanced(%%) **Type**: -
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abonard 260.1 91 === [[Best: Brain Entropy in space and time>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutBEst||rel=" noopener noreferrer" target="_blank"]] ===
abonard 259.1 92
abonard 260.1 93 **Level**: advanced(%%) **Type**: -
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abonard 261.1 95 === [[Epileptogenic Zone Fingerprint>>https://neuroimage.usc.edu/brainstorm/Tutorials/EZFingerprint||rel=" noopener noreferrer" target="_blank"]] ===
abonard 260.1 96
abonard 261.1 97 **Level**: advanced(%%) **Type**: -
98
abonard 262.1 99 === [[SSP Cookbook>>https://neuroimage.usc.edu/brainstorm/Tutorials/SSPCookbook||rel=" noopener noreferrer" target="_blank"]] ===
abonard 261.1 100
abonard 262.1 101 **Level**: advanced(%%) **Type**: -
102
abonard 263.1 103 === [[Elekta-Neuromag tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag||rel=" noopener noreferrer" target="_blank"]] ===
abonard 262.1 104
abonard 263.1 105 **Level**: advanced(%%) **Type**: -
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abonard 264.1 107 === [[Using BrainVISA>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainVisa||rel=" noopener noreferrer" target="_blank"]] ===
abonard 263.1 108
abonard 264.1 109 **Level**: advanced(%%) **Type**: -
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abonard 265.1 111 === [[MEG median nerve tutorial (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/MedianNerveCtf||rel=" noopener noreferrer" target="_blank"]] ===
abonard 264.1 112
abonard 265.1 113 **Level**: advanced(%%) **Type**: -
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abonard 266.1 115 === [[Spike Sorting in Brainstorm>>https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting||rel=" noopener noreferrer" target="_blank"]] ===
abonard 265.1 116
abonard 266.1 117 **Level**: advanced(%%) **Type**: -
118
abonard 267.1 119 === [[Coordinate systems>>https://neuroimage.usc.edu/brainstorm/CoordinateSystems||rel=" noopener noreferrer" target="_blank"]] ===
abonard 266.1 120
abonard 267.1 121 **Level**: advanced(%%) **Type**: -
122
abonard 268.1 123 === [[Real-time head-tracking for adjusting head position>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime||rel=" noopener noreferrer" target="_blank"]] ===
abonard 267.1 124
abonard 268.1 125 **Level**: advanced(%%) **Type**: -
126
abonard 269.1 127 === [[Spectral Parameterization Resolved in Time (SPRiNT)>>https://neuroimage.usc.edu/brainstorm/Tutorials/SPRiNT||rel=" noopener noreferrer" target="_blank"]] ===
abonard 268.1 128
abonard 269.1 129 **Level**: advanced(%%) **Type**: -
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abonard 270.1 131 === [[Montage editor>>https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor||rel=" noopener noreferrer" target="_blank"]] ===
abonard 269.1 132
abonard 270.1 133 **Level**: advanced(%%) **Type**: -
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abonard 271.1 135 === [[Tutorial - Head Motion>>https://neuroimage.usc.edu/brainstorm/Tutorials/HeadMotion||rel=" noopener noreferrer" target="_blank"]] ===
abonard 270.1 136
abonard 271.1 137 **Level**: advanced(%%) **Type**: -
138
abonard 272.1 139 === [[Virtual Fiber Tracks for Connectivity Visualization>>https://neuroimage.usc.edu/brainstorm/Tutorials/FiberConnectivity||rel=" noopener noreferrer" target="_blank"]] ===
abonard 271.1 140
abonard 272.1 141 **Level**: advanced(%%) **Type**: -
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abonard 273.1 143 === [[MEG visual tutorial: Single subject (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle||rel=" noopener noreferrer" target="_blank"]] ===
abonard 272.1 144
abonard 273.1 145 **Level**: advanced(%%) **Type**: -
146
abonard 274.1 147 === [[Digitize EEG sensor locations and head shape>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutDigitize||rel=" noopener noreferrer" target="_blank"]] ===
abonard 273.1 148
abonard 274.1 149 **Level**: advanced(%%) **Type**: -
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abonard 275.1 151 === [[MEG visual tutorial: Group analysis (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup||rel=" noopener noreferrer" target="_blank"]] ===
abonard 274.1 152
abonard 275.1 153 **Level**: advanced(%%) **Type**: -
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abonard 276.1 155 === [[Converting to Brainstorm Events>>https://neuroimage.usc.edu/brainstorm/e-phys/ConvertToBrainstormEvents||rel=" noopener noreferrer" target="_blank"]] ===
abonard 275.1 156
abonard 276.1 157 **Level**: advanced(%%) **Type**: -
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abonard 277.1 159 === [[Synchronization with eye tracker (event transfer)>>https://neuroimage.usc.edu/brainstorm/Tutorials/EyetrackSynchro||rel=" noopener noreferrer" target="_blank"]] ===
abonard 276.1 160
abonard 277.1 161 **Level**: advanced(%%) **Type**: -
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abonard 278.1 163 === [[Using the anatomy templates>>https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 277.1 164
abonard 278.1 165 **Level**: advanced(%%) **Type**: -
166
abonard 279.1 167 === [[Fitting dipoles with FieldTrip>>https://neuroimage.usc.edu/brainstorm/Tutorials/DipoleFitting||rel=" noopener noreferrer" target="_blank"]] ===
abonard 278.1 168
abonard 279.1 169 **Level**: advanced(%%) **Type**: -
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abonard 280.1 171 === [[Deriving LFP signals from raw signals>>https://neuroimage.usc.edu/brainstorm/e-phys/RawToLFP||rel=" noopener noreferrer" target="_blank"]] ===
abonard 279.1 172
abonard 280.1 173 **Level**: advanced(%%) **Type**: -
174
abonard 281.1 175 === [[MEG current phantom (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomCtf||rel=" noopener noreferrer" target="_blank"]] ===
abonard 280.1 176
abonard 281.1 177 **Level**: advanced(%%) **Type**: -
178
abonard 282.1 179 === [[Resting state recordings from the OMEGA database>>https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega||rel=" noopener noreferrer" target="_blank"]] ===
abonard 281.1 180
abonard 282.1 181 **Level**: advanced(%%) **Type**: -
182
abonard 283.1 183 === [[Realistic head model: FEM with DUNEuro>>https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro||rel=" noopener noreferrer" target="_blank"]] ===
abonard 282.1 184
abonard 283.1 185 **Level**: advanced(%%) **Type**: -
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abonard 284.1 187 === [[Functions for Basic e-phys>>https://neuroimage.usc.edu/brainstorm/e-phys/functions||rel=" noopener noreferrer" target="_blank"]] ===
abonard 283.1 188
abonard 284.1 189 **Level**: advanced(%%) **Type**: -
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abonard 285.1 191 === [[MRI segmentation with FastSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegFastSurfer||rel=" noopener noreferrer" target="_blank"]] ===
abonard 284.1 192
abonard 285.1 193 **Level**: advanced(%%) **Type**: -
194
abonard 286.1 195 === [[ECoG/sEEG tutorial>>https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG||rel=" noopener noreferrer" target="_blank"]] ===
abonard 285.1 196
abonard 286.1 197 **Level**: advanced(%%) **Type**: -
198
abonard 287.1 199 === [[Using FreeSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer||rel=" noopener noreferrer" target="_blank"]] ===
abonard 286.1 200
abonard 287.1 201 **Level**: advanced(%%) **Type**: -
202
abonard 288.1 203 === [[Granger causality>>https://neuroimage.usc.edu/brainstorm/GrangerCausality||rel=" noopener noreferrer" target="_blank"]] ===
abonard 287.1 204
abonard 288.1 205 **Level**: advanced(%%) **Type**: -
206
abonard 289.1 207 === [[EEG and epilepsy>>https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 288.1 208
abonard 289.1 209 **Level**: advanced(%%) **Type**: -
210
abonard 290.1 211 === [[Yokogawa/KIT tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/Yokogawa||rel=" noopener noreferrer" target="_blank"]] ===
abonard 289.1 212
abonard 290.1 213 **Level**: advanced(%%) **Type**: -
214
abonard 291.1 215 === [[MRI segmentation with CIVET>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCIVET||rel=" noopener noreferrer" target="_blank"]] ===
abonard 290.1 216
abonard 291.1 217 **Level**: advanced(%%) **Type**: -
218
abonard 292.1 219 === [[Fitting Oscillations and One-Over-F (FOOOF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/Fooof||rel=" noopener noreferrer" target="_blank"]] ===
abonard 291.1 220
abonard 292.1 221 **Level**: advanced(%%) **Type**: -
222
abonard 293.1 223 === [[Human Connectome Project: Resting-state MEG>>https://neuroimage.usc.edu/brainstorm/Tutorials/HCP-MEG||rel=" noopener noreferrer" target="_blank"]] ===
abonard 292.1 224
abonard 293.1 225 **Level**: advanced(%%) **Type**: -
226
abonard 294.1 227 === [[T1-MRI Segmentation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite||rel=" noopener noreferrer" target="_blank"]] ===
abonard 293.1 228
abonard 294.1 229 **Level**: advanced(%%) **Type**: -
230
abonard 295.1 231 === [[Connectivity Graphs>>https://neuroimage.usc.edu/brainstorm/Tutorials/ConnectivityGraph||rel=" noopener noreferrer" target="_blank"]] ===
abonard 294.1 232
abonard 295.1 233 **Level**: advanced(%%) **Type**: -
234
abonard 296.1 235 === [[Export raw files in BIDS format>>https://neuroimage.usc.edu/brainstorm/ExportBids||rel=" noopener noreferrer" target="_blank"]] ===
abonard 295.1 236
abonard 296.1 237 **Level**: advanced(%%) **Type**: -
238
abonard 297.1 239 === [[How to write your own process>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutUserProcess||rel=" noopener noreferrer" target="_blank"]] ===
abonard 296.1 240
abonard 297.1 241 **Level**: advanced(%%) **Type**: -
242
abonard 298.1 243 === [[FEM tensors estimation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemTensors||rel=" noopener noreferrer" target="_blank"]] ===
abonard 297.1 244
abonard 298.1 245 **Level**: advanced(%%) **Type**: -
246
abonard 299.1 247 === [[MRI Segmentation with CAT12>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12||rel=" noopener noreferrer" target="_blank"]] ===
abonard 298.1 248
abonard 299.1 249 **Level**: advanced(%%) **Type**: -
250
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