Wiki source code of Brainstorm

Version 117.1 by abonard on 2025/04/10 15:14
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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 68.1 5 * ((( ==== **[[Intermediate >>||anchor = "HIntermediate-1"]]** ==== )))
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abonard 72.1 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 64.1 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 64.1 18 **Level**: beginner(%%) **Type**: interactive tutorial
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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 65.1 22 === [[Brainstorm: Imaging neural activity at the speed of brain>>https://www.youtube.com/watch?v=30eFJUrRcN4||rel=" noopener noreferrer" target="_blank"]] ===
abonard 64.1 23
abonard 65.1 24 **Level**: beginner(%%) **Type**: video tutorial
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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 66.1 30 === [[Starting a new study – Import the subject anatomy>>https://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 65.1 31
abonard 66.1 32 **Level**: beginner(%%) **Type**: interactive tutorial
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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 67.1 35 === [[Introduction tutorials>>https://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction||rel=" noopener noreferrer" target="_blank"]] ===
abonard 66.1 36
abonard 67.1 37 **Level**: beginner(%%) **Type**: -
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abonard 68.1 39 === **Intermediate** ===
abonard 67.1 40
abonard 68.1 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 69.1 45 === [[Reviewing – Continuous recordings>>https://neuroimage.usc.edu/brainstorm/Tutorials/ReviewRaw||rel=" noopener noreferrer" target="_blank"]] ===
abonard 68.1 46
abonard 69.1 47 **Level**: intermediate(%%) **Type**: interactive tutorial
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abonard 70.1 49 === [[Reviewing – Multiple windows>>https://neuroimage.usc.edu/brainstorm/Tutorials/MultipleWindows||rel=" noopener noreferrer" target="_blank"]] ===
abonard 69.1 50
abonard 70.1 51 **Level**: intermediate(%%) **Type**: interactive tutorial
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abonard 71.1 53 === [[Reviewing – Channel file / MRI registration>>https://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile||rel=" noopener noreferrer" target="_blank"]] ===
abonard 70.1 54
abonard 71.1 55 **Level**: intermediate(%%) **Type**: interactive tutorial
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abonard 72.1 57 === **Advanced** ===
abonard 71.1 58
abonard 72.1 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 73.1 63 === [[MEG current phantom (Elekta-Neuromag)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomElekta||rel=" noopener noreferrer" target="_blank"]] ===
abonard 72.1 64
abonard 73.1 65 **Level**: advanced(%%) **Type**: -
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abonard 74.1 67 === [[Plugins>>https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins||rel=" noopener noreferrer" target="_blank"]] ===
abonard 73.1 68
abonard 74.1 69 **Level**: advanced(%%) **Type**: -
70
abonard 75.1 71 === [[FEM mesh generation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMesh||rel=" noopener noreferrer" target="_blank"]] ===
abonard 74.1 72
abonard 75.1 73 **Level**: advanced(%%) **Type**: -
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abonard 76.1 75 === [[Group analysis: Subject coregistration>>https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects||rel=" noopener noreferrer" target="_blank"]] ===
abonard 75.1 76
abonard 76.1 77 **Level**: advanced(%%) **Type**: -
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abonard 77.1 79 === [[FEM advanced tutorial with MEG/EEG Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMedianNerve||rel=" noopener noreferrer" target="_blank"]] ===
abonard 76.1 80
abonard 77.1 81 **Level**: advanced(%%) **Type**: -
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abonard 78.1 83 === [[Connectivity>>https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity||rel=" noopener noreferrer" target="_blank"]] ===
abonard 77.1 84
abonard 78.1 85 **Level**: advanced(%%) **Type**: -
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abonard 79.1 87 === [[Corticomuscular coherence (CTF MEG)>>https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence||rel=" noopener noreferrer" target="_blank"]] ===
abonard 78.1 88
abonard 79.1 89 **Level**: advanced(%%) **Type**: -
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abonard 80.1 91 === [[Best: Brain Entropy in space and time>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutBEst||rel=" noopener noreferrer" target="_blank"]] ===
abonard 79.1 92
abonard 80.1 93 **Level**: advanced(%%) **Type**: -
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abonard 81.1 95 === [[Epileptogenic Zone Fingerprint>>https://neuroimage.usc.edu/brainstorm/Tutorials/EZFingerprint||rel=" noopener noreferrer" target="_blank"]] ===
abonard 80.1 96
abonard 81.1 97 **Level**: advanced(%%) **Type**: -
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abonard 82.1 99 === [[SSP Cookbook>>https://neuroimage.usc.edu/brainstorm/Tutorials/SSPCookbook||rel=" noopener noreferrer" target="_blank"]] ===
abonard 81.1 100
abonard 82.1 101 **Level**: advanced(%%) **Type**: -
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abonard 83.1 103 === [[Elekta-Neuromag tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag||rel=" noopener noreferrer" target="_blank"]] ===
abonard 82.1 104
abonard 83.1 105 **Level**: advanced(%%) **Type**: -
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abonard 84.1 107 === [[Using BrainVISA>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainVisa||rel=" noopener noreferrer" target="_blank"]] ===
abonard 83.1 108
abonard 84.1 109 **Level**: advanced(%%) **Type**: -
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abonard 85.1 111 === [[MEG median nerve tutorial (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/MedianNerveCtf||rel=" noopener noreferrer" target="_blank"]] ===
abonard 84.1 112
abonard 85.1 113 **Level**: advanced(%%) **Type**: -
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abonard 86.1 115 === [[Spike Sorting in Brainstorm>>https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting||rel=" noopener noreferrer" target="_blank"]] ===
abonard 85.1 116
abonard 86.1 117 **Level**: advanced(%%) **Type**: -
118
abonard 87.1 119 === [[Coordinate systems>>https://neuroimage.usc.edu/brainstorm/CoordinateSystems||rel=" noopener noreferrer" target="_blank"]] ===
abonard 86.1 120
abonard 87.1 121 **Level**: advanced(%%) **Type**: -
122
abonard 88.1 123 === [[Real-time head-tracking for adjusting head position>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime||rel=" noopener noreferrer" target="_blank"]] ===
abonard 87.1 124
abonard 88.1 125 **Level**: advanced(%%) **Type**: -
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abonard 89.1 127 === [[Spectral Parameterization Resolved in Time (SPRiNT)>>https://neuroimage.usc.edu/brainstorm/Tutorials/SPRiNT||rel=" noopener noreferrer" target="_blank"]] ===
abonard 88.1 128
abonard 89.1 129 **Level**: advanced(%%) **Type**: -
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abonard 90.1 131 === [[Montage editor>>https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor||rel=" noopener noreferrer" target="_blank"]] ===
abonard 89.1 132
abonard 90.1 133 **Level**: advanced(%%) **Type**: -
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abonard 91.1 135 === [[Tutorial - Head Motion>>https://neuroimage.usc.edu/brainstorm/Tutorials/HeadMotion||rel=" noopener noreferrer" target="_blank"]] ===
abonard 90.1 136
abonard 91.1 137 **Level**: advanced(%%) **Type**: -
138
abonard 92.1 139 === [[Virtual Fiber Tracks for Connectivity Visualization>>https://neuroimage.usc.edu/brainstorm/Tutorials/FiberConnectivity||rel=" noopener noreferrer" target="_blank"]] ===
abonard 91.1 140
abonard 92.1 141 **Level**: advanced(%%) **Type**: -
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abonard 93.1 143 === [[MEG visual tutorial: Single subject (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle||rel=" noopener noreferrer" target="_blank"]] ===
abonard 92.1 144
abonard 93.1 145 **Level**: advanced(%%) **Type**: -
146
abonard 94.1 147 === [[Digitize EEG sensor locations and head shape>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutDigitize||rel=" noopener noreferrer" target="_blank"]] ===
abonard 93.1 148
abonard 94.1 149 **Level**: advanced(%%) **Type**: -
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abonard 95.1 151 === [[MEG visual tutorial: Group analysis (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup||rel=" noopener noreferrer" target="_blank"]] ===
abonard 94.1 152
abonard 95.1 153 **Level**: advanced(%%) **Type**: -
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abonard 96.1 155 === [[Converting to Brainstorm Events>>https://neuroimage.usc.edu/brainstorm/e-phys/ConvertToBrainstormEvents||rel=" noopener noreferrer" target="_blank"]] ===
abonard 95.1 156
abonard 96.1 157 **Level**: advanced(%%) **Type**: -
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abonard 97.1 159 === [[Synchronization with eye tracker (event transfer)>>https://neuroimage.usc.edu/brainstorm/Tutorials/EyetrackSynchro||rel=" noopener noreferrer" target="_blank"]] ===
abonard 96.1 160
abonard 97.1 161 **Level**: advanced(%%) **Type**: -
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abonard 98.1 163 === [[Using the anatomy templates>>https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 97.1 164
abonard 98.1 165 **Level**: advanced(%%) **Type**: -
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abonard 99.1 167 === [[Fitting dipoles with FieldTrip>>https://neuroimage.usc.edu/brainstorm/Tutorials/DipoleFitting||rel=" noopener noreferrer" target="_blank"]] ===
abonard 98.1 168
abonard 99.1 169 **Level**: advanced(%%) **Type**: -
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abonard 100.1 171 === [[Deriving LFP signals from raw signals>>https://neuroimage.usc.edu/brainstorm/e-phys/RawToLFP||rel=" noopener noreferrer" target="_blank"]] ===
abonard 99.1 172
abonard 100.1 173 **Level**: advanced(%%) **Type**: -
174
abonard 101.1 175 === [[MEG current phantom (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomCtf||rel=" noopener noreferrer" target="_blank"]] ===
abonard 100.1 176
abonard 101.1 177 **Level**: advanced(%%) **Type**: -
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abonard 102.1 179 === [[Resting state recordings from the OMEGA database>>https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega||rel=" noopener noreferrer" target="_blank"]] ===
abonard 101.1 180
abonard 102.1 181 **Level**: advanced(%%) **Type**: -
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abonard 103.1 183 === [[Realistic head model: FEM with DUNEuro>>https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro||rel=" noopener noreferrer" target="_blank"]] ===
abonard 102.1 184
abonard 103.1 185 **Level**: advanced(%%) **Type**: -
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abonard 104.1 187 === [[Functions for Basic e-phys>>https://neuroimage.usc.edu/brainstorm/e-phys/functions||rel=" noopener noreferrer" target="_blank"]] ===
abonard 103.1 188
abonard 104.1 189 **Level**: advanced(%%) **Type**: -
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abonard 105.1 191 === [[MRI segmentation with FastSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegFastSurfer||rel=" noopener noreferrer" target="_blank"]] ===
abonard 104.1 192
abonard 105.1 193 **Level**: advanced(%%) **Type**: -
194
abonard 106.1 195 === [[ECoG/sEEG tutorial>>https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG||rel=" noopener noreferrer" target="_blank"]] ===
abonard 105.1 196
abonard 106.1 197 **Level**: advanced(%%) **Type**: -
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abonard 107.1 199 === [[Using FreeSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer||rel=" noopener noreferrer" target="_blank"]] ===
abonard 106.1 200
abonard 107.1 201 **Level**: advanced(%%) **Type**: -
202
abonard 108.1 203 === [[Granger causality>>https://neuroimage.usc.edu/brainstorm/GrangerCausality||rel=" noopener noreferrer" target="_blank"]] ===
abonard 107.1 204
abonard 108.1 205 **Level**: advanced(%%) **Type**: -
206
abonard 109.1 207 === [[EEG and epilepsy>>https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 108.1 208
abonard 109.1 209 **Level**: advanced(%%) **Type**: -
210
abonard 110.1 211 === [[Yokogawa/KIT tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/Yokogawa||rel=" noopener noreferrer" target="_blank"]] ===
abonard 109.1 212
abonard 110.1 213 **Level**: advanced(%%) **Type**: -
214
abonard 111.1 215 === [[MRI segmentation with CIVET>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCIVET||rel=" noopener noreferrer" target="_blank"]] ===
abonard 110.1 216
abonard 111.1 217 **Level**: advanced(%%) **Type**: -
218
abonard 112.1 219 === [[Fitting Oscillations and One-Over-F (FOOOF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/Fooof||rel=" noopener noreferrer" target="_blank"]] ===
abonard 111.1 220
abonard 112.1 221 **Level**: advanced(%%) **Type**: -
222
abonard 113.1 223 === [[Human Connectome Project: Resting-state MEG>>https://neuroimage.usc.edu/brainstorm/Tutorials/HCP-MEG||rel=" noopener noreferrer" target="_blank"]] ===
abonard 112.1 224
abonard 113.1 225 **Level**: advanced(%%) **Type**: -
226
abonard 114.1 227 === [[T1-MRI Segmentation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite||rel=" noopener noreferrer" target="_blank"]] ===
abonard 113.1 228
abonard 114.1 229 **Level**: advanced(%%) **Type**: -
230
abonard 115.1 231 === [[Connectivity Graphs>>https://neuroimage.usc.edu/brainstorm/Tutorials/ConnectivityGraph||rel=" noopener noreferrer" target="_blank"]] ===
abonard 114.1 232
abonard 115.1 233 **Level**: advanced(%%) **Type**: -
234
abonard 116.1 235 === [[Export raw files in BIDS format>>https://neuroimage.usc.edu/brainstorm/ExportBids||rel=" noopener noreferrer" target="_blank"]] ===
abonard 115.1 236
abonard 116.1 237 **Level**: advanced(%%) **Type**: -
238
abonard 117.1 239 === [[How to write your own process>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutUserProcess||rel=" noopener noreferrer" target="_blank"]] ===
abonard 116.1 240
abonard 117.1 241 **Level**: advanced(%%) **Type**: -
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