Wiki source code of Brainstorm

Version 181.1 by abonard on 2025/05/23 13:18
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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 128.1 5 * ((( ==== **[[Intermediate >>||anchor = "HIntermediate-1"]]** ==== )))
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abonard 132.1 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 124.1 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 124.1 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 125.1 22 === [[Brainstorm: Imaging neural activity at the speed of brain>>https://www.youtube.com/watch?v=30eFJUrRcN4||rel=" noopener noreferrer" target="_blank"]] ===
abonard 124.1 23
abonard 125.1 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.
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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 126.1 30 === [[Starting a new study – Import the subject anatomy>>https://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 125.1 31
abonard 126.1 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 127.1 35 === [[Introduction tutorials>>https://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction||rel=" noopener noreferrer" target="_blank"]] ===
abonard 126.1 36
abonard 127.1 37 **Level**: beginner(%%) **Type**: -
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abonard 128.1 39 === **Intermediate** ===
abonard 127.1 40
abonard 128.1 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 129.1 45 === [[Reviewing – Continuous recordings>>https://neuroimage.usc.edu/brainstorm/Tutorials/ReviewRaw||rel=" noopener noreferrer" target="_blank"]] ===
abonard 128.1 46
abonard 129.1 47 **Level**: intermediate(%%) **Type**: interactive tutorial
48
abonard 130.1 49 === [[Reviewing – Multiple windows>>https://neuroimage.usc.edu/brainstorm/Tutorials/MultipleWindows||rel=" noopener noreferrer" target="_blank"]] ===
abonard 129.1 50
abonard 130.1 51 **Level**: intermediate(%%) **Type**: interactive tutorial
52
abonard 131.1 53 === [[Reviewing – Channel file / MRI registration>>https://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile||rel=" noopener noreferrer" target="_blank"]] ===
abonard 130.1 54
abonard 131.1 55 **Level**: intermediate(%%) **Type**: interactive tutorial
56
abonard 132.1 57 === **Advanced** ===
abonard 131.1 58
abonard 132.1 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 133.1 63 === [[MEG current phantom (Elekta-Neuromag)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomElekta||rel=" noopener noreferrer" target="_blank"]] ===
abonard 132.1 64
abonard 133.1 65 **Level**: advanced(%%) **Type**: -
66
abonard 134.1 67 === [[Plugins>>https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins||rel=" noopener noreferrer" target="_blank"]] ===
abonard 133.1 68
abonard 134.1 69 **Level**: advanced(%%) **Type**: -
70
abonard 135.1 71 === [[FEM mesh generation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMesh||rel=" noopener noreferrer" target="_blank"]] ===
abonard 134.1 72
abonard 135.1 73 **Level**: advanced(%%) **Type**: -
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abonard 136.1 75 === [[Group analysis: Subject coregistration>>https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects||rel=" noopener noreferrer" target="_blank"]] ===
abonard 135.1 76
abonard 136.1 77 **Level**: advanced(%%) **Type**: -
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abonard 137.1 79 === [[FEM advanced tutorial with MEG/EEG Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMedianNerve||rel=" noopener noreferrer" target="_blank"]] ===
abonard 136.1 80
abonard 137.1 81 **Level**: advanced(%%) **Type**: -
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abonard 138.1 83 === [[Connectivity>>https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity||rel=" noopener noreferrer" target="_blank"]] ===
abonard 137.1 84
abonard 138.1 85 **Level**: advanced(%%) **Type**: -
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abonard 139.1 87 === [[Corticomuscular coherence (CTF MEG)>>https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence||rel=" noopener noreferrer" target="_blank"]] ===
abonard 138.1 88
abonard 139.1 89 **Level**: advanced(%%) **Type**: -
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abonard 140.1 91 === [[Best: Brain Entropy in space and time>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutBEst||rel=" noopener noreferrer" target="_blank"]] ===
abonard 139.1 92
abonard 140.1 93 **Level**: advanced(%%) **Type**: -
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abonard 141.1 95 === [[Epileptogenic Zone Fingerprint>>https://neuroimage.usc.edu/brainstorm/Tutorials/EZFingerprint||rel=" noopener noreferrer" target="_blank"]] ===
abonard 140.1 96
abonard 141.1 97 **Level**: advanced(%%) **Type**: -
98
abonard 142.1 99 === [[SSP Cookbook>>https://neuroimage.usc.edu/brainstorm/Tutorials/SSPCookbook||rel=" noopener noreferrer" target="_blank"]] ===
abonard 141.1 100
abonard 142.1 101 **Level**: advanced(%%) **Type**: -
102
abonard 143.1 103 === [[Elekta-Neuromag tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag||rel=" noopener noreferrer" target="_blank"]] ===
abonard 142.1 104
abonard 143.1 105 **Level**: advanced(%%) **Type**: -
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abonard 144.1 107 === [[Using BrainVISA>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainVisa||rel=" noopener noreferrer" target="_blank"]] ===
abonard 143.1 108
abonard 144.1 109 **Level**: advanced(%%) **Type**: -
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abonard 145.1 111 === [[MEG median nerve tutorial (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/MedianNerveCtf||rel=" noopener noreferrer" target="_blank"]] ===
abonard 144.1 112
abonard 145.1 113 **Level**: advanced(%%) **Type**: -
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abonard 146.1 115 === [[Spike Sorting in Brainstorm>>https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting||rel=" noopener noreferrer" target="_blank"]] ===
abonard 145.1 116
abonard 146.1 117 **Level**: advanced(%%) **Type**: -
118
abonard 147.1 119 === [[Coordinate systems>>https://neuroimage.usc.edu/brainstorm/CoordinateSystems||rel=" noopener noreferrer" target="_blank"]] ===
abonard 146.1 120
abonard 147.1 121 **Level**: advanced(%%) **Type**: -
122
abonard 148.1 123 === [[Real-time head-tracking for adjusting head position>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime||rel=" noopener noreferrer" target="_blank"]] ===
abonard 147.1 124
abonard 148.1 125 **Level**: advanced(%%) **Type**: -
126
abonard 149.1 127 === [[Spectral Parameterization Resolved in Time (SPRiNT)>>https://neuroimage.usc.edu/brainstorm/Tutorials/SPRiNT||rel=" noopener noreferrer" target="_blank"]] ===
abonard 148.1 128
abonard 149.1 129 **Level**: advanced(%%) **Type**: -
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abonard 150.1 131 === [[Montage editor>>https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor||rel=" noopener noreferrer" target="_blank"]] ===
abonard 149.1 132
abonard 150.1 133 **Level**: advanced(%%) **Type**: -
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abonard 151.1 135 === [[Tutorial - Head Motion>>https://neuroimage.usc.edu/brainstorm/Tutorials/HeadMotion||rel=" noopener noreferrer" target="_blank"]] ===
abonard 150.1 136
abonard 151.1 137 **Level**: advanced(%%) **Type**: -
138
abonard 152.1 139 === [[Virtual Fiber Tracks for Connectivity Visualization>>https://neuroimage.usc.edu/brainstorm/Tutorials/FiberConnectivity||rel=" noopener noreferrer" target="_blank"]] ===
abonard 151.1 140
abonard 152.1 141 **Level**: advanced(%%) **Type**: -
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abonard 153.1 143 === [[MEG visual tutorial: Single subject (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle||rel=" noopener noreferrer" target="_blank"]] ===
abonard 152.1 144
abonard 153.1 145 **Level**: advanced(%%) **Type**: -
146
abonard 154.1 147 === [[Digitize EEG sensor locations and head shape>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutDigitize||rel=" noopener noreferrer" target="_blank"]] ===
abonard 153.1 148
abonard 154.1 149 **Level**: advanced(%%) **Type**: -
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abonard 155.1 151 === [[MEG visual tutorial: Group analysis (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup||rel=" noopener noreferrer" target="_blank"]] ===
abonard 154.1 152
abonard 155.1 153 **Level**: advanced(%%) **Type**: -
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abonard 156.1 155 === [[Converting to Brainstorm Events>>https://neuroimage.usc.edu/brainstorm/e-phys/ConvertToBrainstormEvents||rel=" noopener noreferrer" target="_blank"]] ===
abonard 155.1 156
abonard 156.1 157 **Level**: advanced(%%) **Type**: -
158
abonard 157.1 159 === [[Synchronization with eye tracker (event transfer)>>https://neuroimage.usc.edu/brainstorm/Tutorials/EyetrackSynchro||rel=" noopener noreferrer" target="_blank"]] ===
abonard 156.1 160
abonard 157.1 161 **Level**: advanced(%%) **Type**: -
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abonard 158.1 163 === [[Using the anatomy templates>>https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 157.1 164
abonard 158.1 165 **Level**: advanced(%%) **Type**: -
166
abonard 159.1 167 === [[Fitting dipoles with FieldTrip>>https://neuroimage.usc.edu/brainstorm/Tutorials/DipoleFitting||rel=" noopener noreferrer" target="_blank"]] ===
abonard 158.1 168
abonard 159.1 169 **Level**: advanced(%%) **Type**: -
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abonard 160.1 171 === [[Deriving LFP signals from raw signals>>https://neuroimage.usc.edu/brainstorm/e-phys/RawToLFP||rel=" noopener noreferrer" target="_blank"]] ===
abonard 159.1 172
abonard 160.1 173 **Level**: advanced(%%) **Type**: -
174
abonard 161.1 175 === [[MEG current phantom (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomCtf||rel=" noopener noreferrer" target="_blank"]] ===
abonard 160.1 176
abonard 161.1 177 **Level**: advanced(%%) **Type**: -
178
abonard 162.1 179 === [[Resting state recordings from the OMEGA database>>https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega||rel=" noopener noreferrer" target="_blank"]] ===
abonard 161.1 180
abonard 162.1 181 **Level**: advanced(%%) **Type**: -
182
abonard 163.1 183 === [[Realistic head model: FEM with DUNEuro>>https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro||rel=" noopener noreferrer" target="_blank"]] ===
abonard 162.1 184
abonard 163.1 185 **Level**: advanced(%%) **Type**: -
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abonard 164.1 187 === [[Functions for Basic e-phys>>https://neuroimage.usc.edu/brainstorm/e-phys/functions||rel=" noopener noreferrer" target="_blank"]] ===
abonard 163.1 188
abonard 164.1 189 **Level**: advanced(%%) **Type**: -
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abonard 165.1 191 === [[MRI segmentation with FastSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegFastSurfer||rel=" noopener noreferrer" target="_blank"]] ===
abonard 164.1 192
abonard 165.1 193 **Level**: advanced(%%) **Type**: -
194
abonard 166.1 195 === [[ECoG/sEEG tutorial>>https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG||rel=" noopener noreferrer" target="_blank"]] ===
abonard 165.1 196
abonard 166.1 197 **Level**: advanced(%%) **Type**: -
198
abonard 167.1 199 === [[Using FreeSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer||rel=" noopener noreferrer" target="_blank"]] ===
abonard 166.1 200
abonard 167.1 201 **Level**: advanced(%%) **Type**: -
202
abonard 168.1 203 === [[Granger causality>>https://neuroimage.usc.edu/brainstorm/GrangerCausality||rel=" noopener noreferrer" target="_blank"]] ===
abonard 167.1 204
abonard 168.1 205 **Level**: advanced(%%) **Type**: -
206
abonard 169.1 207 === [[EEG and epilepsy>>https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 168.1 208
abonard 169.1 209 **Level**: advanced(%%) **Type**: -
210
abonard 170.1 211 === [[Yokogawa/KIT tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/Yokogawa||rel=" noopener noreferrer" target="_blank"]] ===
abonard 169.1 212
abonard 170.1 213 **Level**: advanced(%%) **Type**: -
214
abonard 171.1 215 === [[MRI segmentation with CIVET>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCIVET||rel=" noopener noreferrer" target="_blank"]] ===
abonard 170.1 216
abonard 171.1 217 **Level**: advanced(%%) **Type**: -
218
abonard 172.1 219 === [[Fitting Oscillations and One-Over-F (FOOOF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/Fooof||rel=" noopener noreferrer" target="_blank"]] ===
abonard 171.1 220
abonard 172.1 221 **Level**: advanced(%%) **Type**: -
222
abonard 173.1 223 === [[Human Connectome Project: Resting-state MEG>>https://neuroimage.usc.edu/brainstorm/Tutorials/HCP-MEG||rel=" noopener noreferrer" target="_blank"]] ===
abonard 172.1 224
abonard 173.1 225 **Level**: advanced(%%) **Type**: -
226
abonard 174.1 227 === [[T1-MRI Segmentation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite||rel=" noopener noreferrer" target="_blank"]] ===
abonard 173.1 228
abonard 174.1 229 **Level**: advanced(%%) **Type**: -
230
abonard 175.1 231 === [[Connectivity Graphs>>https://neuroimage.usc.edu/brainstorm/Tutorials/ConnectivityGraph||rel=" noopener noreferrer" target="_blank"]] ===
abonard 174.1 232
abonard 175.1 233 **Level**: advanced(%%) **Type**: -
234
abonard 176.1 235 === [[Export raw files in BIDS format>>https://neuroimage.usc.edu/brainstorm/ExportBids||rel=" noopener noreferrer" target="_blank"]] ===
abonard 175.1 236
abonard 176.1 237 **Level**: advanced(%%) **Type**: -
238
abonard 177.1 239 === [[How to write your own process>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutUserProcess||rel=" noopener noreferrer" target="_blank"]] ===
abonard 176.1 240
abonard 177.1 241 **Level**: advanced(%%) **Type**: -
242
abonard 178.1 243 === [[FEM tensors estimation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemTensors||rel=" noopener noreferrer" target="_blank"]] ===
abonard 177.1 244
abonard 178.1 245 **Level**: advanced(%%) **Type**: -
246
abonard 179.1 247 === [[MRI Segmentation with CAT12>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12||rel=" noopener noreferrer" target="_blank"]] ===
abonard 178.1 248
abonard 179.1 249 **Level**: advanced(%%) **Type**: -
250
abonard 180.1 251 === [[Export volume source maps to SPM8 / SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm8||rel=" noopener noreferrer" target="_blank"]] ===
abonard 179.1 252
abonard 180.1 253 **Level**: advanced(%%) **Type**: -
254
abonard 181.1 255 === [[NIRS data importation, visualization and response estimate in the optode space>>https://neuroimage.usc.edu/brainstorm/Tutorials/NIRSFingerTapping||rel=" noopener noreferrer" target="_blank"]] ===
abonard 180.1 256
abonard 181.1 257 **Level**: advanced(%%) **Type**: -
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