Wiki source code of Brainstorm

Version 240.1 by abonard on 2025/06/03 11:02
Hide last authors
adavison 1.1 1
2
abonard 3.1 3 * ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
jessicamitchell 2.1 4
abonard 188.1 5 * ((( ==== **[[Intermediate >>||anchor = "HIntermediate-1"]]** ==== )))
6
abonard 192.1 7 * ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
8
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 184.1 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 184.1 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 185.1 22 === [[Brainstorm: Imaging neural activity at the speed of brain>>https://www.youtube.com/watch?v=30eFJUrRcN4||rel=" noopener noreferrer" target="_blank"]] ===
abonard 184.1 23
abonard 185.1 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 186.1 30 === [[Starting a new study – Import the subject anatomy>>https://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 185.1 31
abonard 186.1 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 187.1 35 === [[Introduction tutorials>>https://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction||rel=" noopener noreferrer" target="_blank"]] ===
abonard 186.1 36
abonard 187.1 37 **Level**: beginner(%%) **Type**: -
38
abonard 188.1 39 === **Intermediate** ===
abonard 187.1 40
abonard 188.1 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 189.1 45 === [[Reviewing – Continuous recordings>>https://neuroimage.usc.edu/brainstorm/Tutorials/ReviewRaw||rel=" noopener noreferrer" target="_blank"]] ===
abonard 188.1 46
abonard 189.1 47 **Level**: intermediate(%%) **Type**: interactive tutorial
48
abonard 190.1 49 === [[Reviewing – Multiple windows>>https://neuroimage.usc.edu/brainstorm/Tutorials/MultipleWindows||rel=" noopener noreferrer" target="_blank"]] ===
abonard 189.1 50
abonard 190.1 51 **Level**: intermediate(%%) **Type**: interactive tutorial
52
abonard 191.1 53 === [[Reviewing – Channel file / MRI registration>>https://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile||rel=" noopener noreferrer" target="_blank"]] ===
abonard 190.1 54
abonard 191.1 55 **Level**: intermediate(%%) **Type**: interactive tutorial
56
abonard 192.1 57 === **Advanced** ===
abonard 191.1 58
abonard 192.1 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 193.1 63 === [[MEG current phantom (Elekta-Neuromag)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomElekta||rel=" noopener noreferrer" target="_blank"]] ===
abonard 192.1 64
abonard 193.1 65 **Level**: advanced(%%) **Type**: -
66
abonard 194.1 67 === [[Plugins>>https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins||rel=" noopener noreferrer" target="_blank"]] ===
abonard 193.1 68
abonard 194.1 69 **Level**: advanced(%%) **Type**: -
70
abonard 195.1 71 === [[FEM mesh generation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMesh||rel=" noopener noreferrer" target="_blank"]] ===
abonard 194.1 72
abonard 195.1 73 **Level**: advanced(%%) **Type**: -
74
abonard 196.1 75 === [[Group analysis: Subject coregistration>>https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects||rel=" noopener noreferrer" target="_blank"]] ===
abonard 195.1 76
abonard 196.1 77 **Level**: advanced(%%) **Type**: -
78
abonard 197.1 79 === [[FEM advanced tutorial with MEG/EEG Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMedianNerve||rel=" noopener noreferrer" target="_blank"]] ===
abonard 196.1 80
abonard 197.1 81 **Level**: advanced(%%) **Type**: -
82
abonard 198.1 83 === [[Connectivity>>https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity||rel=" noopener noreferrer" target="_blank"]] ===
abonard 197.1 84
abonard 198.1 85 **Level**: advanced(%%) **Type**: -
86
abonard 199.1 87 === [[Corticomuscular coherence (CTF MEG)>>https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence||rel=" noopener noreferrer" target="_blank"]] ===
abonard 198.1 88
abonard 199.1 89 **Level**: advanced(%%) **Type**: -
90
abonard 200.1 91 === [[Best: Brain Entropy in space and time>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutBEst||rel=" noopener noreferrer" target="_blank"]] ===
abonard 199.1 92
abonard 200.1 93 **Level**: advanced(%%) **Type**: -
94
abonard 201.1 95 === [[Epileptogenic Zone Fingerprint>>https://neuroimage.usc.edu/brainstorm/Tutorials/EZFingerprint||rel=" noopener noreferrer" target="_blank"]] ===
abonard 200.1 96
abonard 201.1 97 **Level**: advanced(%%) **Type**: -
98
abonard 202.1 99 === [[SSP Cookbook>>https://neuroimage.usc.edu/brainstorm/Tutorials/SSPCookbook||rel=" noopener noreferrer" target="_blank"]] ===
abonard 201.1 100
abonard 202.1 101 **Level**: advanced(%%) **Type**: -
102
abonard 203.1 103 === [[Elekta-Neuromag tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag||rel=" noopener noreferrer" target="_blank"]] ===
abonard 202.1 104
abonard 203.1 105 **Level**: advanced(%%) **Type**: -
106
abonard 204.1 107 === [[Using BrainVISA>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainVisa||rel=" noopener noreferrer" target="_blank"]] ===
abonard 203.1 108
abonard 204.1 109 **Level**: advanced(%%) **Type**: -
110
abonard 205.1 111 === [[MEG median nerve tutorial (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/MedianNerveCtf||rel=" noopener noreferrer" target="_blank"]] ===
abonard 204.1 112
abonard 205.1 113 **Level**: advanced(%%) **Type**: -
114
abonard 206.1 115 === [[Spike Sorting in Brainstorm>>https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting||rel=" noopener noreferrer" target="_blank"]] ===
abonard 205.1 116
abonard 206.1 117 **Level**: advanced(%%) **Type**: -
118
abonard 207.1 119 === [[Coordinate systems>>https://neuroimage.usc.edu/brainstorm/CoordinateSystems||rel=" noopener noreferrer" target="_blank"]] ===
abonard 206.1 120
abonard 207.1 121 **Level**: advanced(%%) **Type**: -
122
abonard 208.1 123 === [[Real-time head-tracking for adjusting head position>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime||rel=" noopener noreferrer" target="_blank"]] ===
abonard 207.1 124
abonard 208.1 125 **Level**: advanced(%%) **Type**: -
126
abonard 209.1 127 === [[Spectral Parameterization Resolved in Time (SPRiNT)>>https://neuroimage.usc.edu/brainstorm/Tutorials/SPRiNT||rel=" noopener noreferrer" target="_blank"]] ===
abonard 208.1 128
abonard 209.1 129 **Level**: advanced(%%) **Type**: -
130
abonard 210.1 131 === [[Montage editor>>https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor||rel=" noopener noreferrer" target="_blank"]] ===
abonard 209.1 132
abonard 210.1 133 **Level**: advanced(%%) **Type**: -
134
abonard 211.1 135 === [[Tutorial - Head Motion>>https://neuroimage.usc.edu/brainstorm/Tutorials/HeadMotion||rel=" noopener noreferrer" target="_blank"]] ===
abonard 210.1 136
abonard 211.1 137 **Level**: advanced(%%) **Type**: -
138
abonard 212.1 139 === [[Virtual Fiber Tracks for Connectivity Visualization>>https://neuroimage.usc.edu/brainstorm/Tutorials/FiberConnectivity||rel=" noopener noreferrer" target="_blank"]] ===
abonard 211.1 140
abonard 212.1 141 **Level**: advanced(%%) **Type**: -
142
abonard 213.1 143 === [[MEG visual tutorial: Single subject (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle||rel=" noopener noreferrer" target="_blank"]] ===
abonard 212.1 144
abonard 213.1 145 **Level**: advanced(%%) **Type**: -
146
abonard 214.1 147 === [[Digitize EEG sensor locations and head shape>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutDigitize||rel=" noopener noreferrer" target="_blank"]] ===
abonard 213.1 148
abonard 214.1 149 **Level**: advanced(%%) **Type**: -
150
abonard 215.1 151 === [[MEG visual tutorial: Group analysis (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup||rel=" noopener noreferrer" target="_blank"]] ===
abonard 214.1 152
abonard 215.1 153 **Level**: advanced(%%) **Type**: -
154
abonard 216.1 155 === [[Converting to Brainstorm Events>>https://neuroimage.usc.edu/brainstorm/e-phys/ConvertToBrainstormEvents||rel=" noopener noreferrer" target="_blank"]] ===
abonard 215.1 156
abonard 216.1 157 **Level**: advanced(%%) **Type**: -
158
abonard 217.1 159 === [[Synchronization with eye tracker (event transfer)>>https://neuroimage.usc.edu/brainstorm/Tutorials/EyetrackSynchro||rel=" noopener noreferrer" target="_blank"]] ===
abonard 216.1 160
abonard 217.1 161 **Level**: advanced(%%) **Type**: -
162
abonard 218.1 163 === [[Using the anatomy templates>>https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 217.1 164
abonard 218.1 165 **Level**: advanced(%%) **Type**: -
166
abonard 219.1 167 === [[Fitting dipoles with FieldTrip>>https://neuroimage.usc.edu/brainstorm/Tutorials/DipoleFitting||rel=" noopener noreferrer" target="_blank"]] ===
abonard 218.1 168
abonard 219.1 169 **Level**: advanced(%%) **Type**: -
170
abonard 220.1 171 === [[Deriving LFP signals from raw signals>>https://neuroimage.usc.edu/brainstorm/e-phys/RawToLFP||rel=" noopener noreferrer" target="_blank"]] ===
abonard 219.1 172
abonard 220.1 173 **Level**: advanced(%%) **Type**: -
174
abonard 221.1 175 === [[MEG current phantom (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomCtf||rel=" noopener noreferrer" target="_blank"]] ===
abonard 220.1 176
abonard 221.1 177 **Level**: advanced(%%) **Type**: -
178
abonard 222.1 179 === [[Resting state recordings from the OMEGA database>>https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega||rel=" noopener noreferrer" target="_blank"]] ===
abonard 221.1 180
abonard 222.1 181 **Level**: advanced(%%) **Type**: -
182
abonard 223.1 183 === [[Realistic head model: FEM with DUNEuro>>https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro||rel=" noopener noreferrer" target="_blank"]] ===
abonard 222.1 184
abonard 223.1 185 **Level**: advanced(%%) **Type**: -
186
abonard 224.1 187 === [[Functions for Basic e-phys>>https://neuroimage.usc.edu/brainstorm/e-phys/functions||rel=" noopener noreferrer" target="_blank"]] ===
abonard 223.1 188
abonard 224.1 189 **Level**: advanced(%%) **Type**: -
190
abonard 225.1 191 === [[MRI segmentation with FastSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegFastSurfer||rel=" noopener noreferrer" target="_blank"]] ===
abonard 224.1 192
abonard 225.1 193 **Level**: advanced(%%) **Type**: -
194
abonard 226.1 195 === [[ECoG/sEEG tutorial>>https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG||rel=" noopener noreferrer" target="_blank"]] ===
abonard 225.1 196
abonard 226.1 197 **Level**: advanced(%%) **Type**: -
198
abonard 227.1 199 === [[Using FreeSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer||rel=" noopener noreferrer" target="_blank"]] ===
abonard 226.1 200
abonard 227.1 201 **Level**: advanced(%%) **Type**: -
202
abonard 228.1 203 === [[Granger causality>>https://neuroimage.usc.edu/brainstorm/GrangerCausality||rel=" noopener noreferrer" target="_blank"]] ===
abonard 227.1 204
abonard 228.1 205 **Level**: advanced(%%) **Type**: -
206
abonard 229.1 207 === [[EEG and epilepsy>>https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy||rel=" noopener noreferrer" target="_blank"]] ===
abonard 228.1 208
abonard 229.1 209 **Level**: advanced(%%) **Type**: -
210
abonard 230.1 211 === [[Yokogawa/KIT tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/Yokogawa||rel=" noopener noreferrer" target="_blank"]] ===
abonard 229.1 212
abonard 230.1 213 **Level**: advanced(%%) **Type**: -
214
abonard 231.1 215 === [[MRI segmentation with CIVET>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCIVET||rel=" noopener noreferrer" target="_blank"]] ===
abonard 230.1 216
abonard 231.1 217 **Level**: advanced(%%) **Type**: -
218
abonard 232.1 219 === [[Fitting Oscillations and One-Over-F (FOOOF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/Fooof||rel=" noopener noreferrer" target="_blank"]] ===
abonard 231.1 220
abonard 232.1 221 **Level**: advanced(%%) **Type**: -
222
abonard 233.1 223 === [[Human Connectome Project: Resting-state MEG>>https://neuroimage.usc.edu/brainstorm/Tutorials/HCP-MEG||rel=" noopener noreferrer" target="_blank"]] ===
abonard 232.1 224
abonard 233.1 225 **Level**: advanced(%%) **Type**: -
226
abonard 234.1 227 === [[T1-MRI Segmentation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite||rel=" noopener noreferrer" target="_blank"]] ===
abonard 233.1 228
abonard 234.1 229 **Level**: advanced(%%) **Type**: -
230
abonard 235.1 231 === [[Connectivity Graphs>>https://neuroimage.usc.edu/brainstorm/Tutorials/ConnectivityGraph||rel=" noopener noreferrer" target="_blank"]] ===
abonard 234.1 232
abonard 235.1 233 **Level**: advanced(%%) **Type**: -
234
abonard 236.1 235 === [[Export raw files in BIDS format>>https://neuroimage.usc.edu/brainstorm/ExportBids||rel=" noopener noreferrer" target="_blank"]] ===
abonard 235.1 236
abonard 236.1 237 **Level**: advanced(%%) **Type**: -
238
abonard 237.1 239 === [[How to write your own process>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutUserProcess||rel=" noopener noreferrer" target="_blank"]] ===
abonard 236.1 240
abonard 237.1 241 **Level**: advanced(%%) **Type**: -
242
abonard 238.1 243 === [[FEM tensors estimation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemTensors||rel=" noopener noreferrer" target="_blank"]] ===
abonard 237.1 244
abonard 238.1 245 **Level**: advanced(%%) **Type**: -
246
abonard 239.1 247 === [[MRI Segmentation with CAT12>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12||rel=" noopener noreferrer" target="_blank"]] ===
abonard 238.1 248
abonard 239.1 249 **Level**: advanced(%%) **Type**: -
250
abonard 240.1 251 === [[Export volume source maps to SPM8 / SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm8||rel=" noopener noreferrer" target="_blank"]] ===
abonard 239.1 252
abonard 240.1 253 **Level**: advanced(%%) **Type**: -
254
255