Changes for page Brainstorm

Last modified by abonard on 2025/04/10 15:14
From version 2.1
edited by jessicamitchell
on 2023/09/11 11:44
Change comment: There is no comment for this version
To version 41.1
edited by abonard
on 2025/04/10 15:04
Change comment: There is no comment for this version

Summary

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1 -XWiki.jessicamitchell
1 +XWiki.abonard
Content
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1 -Available tutorials:
2 2  
3 -=== [[Introduction tutorials>>https://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction||rel=" noopener noreferrer" target="_blank"]] ===
4 4  
5 -//Level: beginner//
3 +* ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
6 6  
7 -=== [[Best: Brain Entropy in space and time>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutBEst||rel=" noopener noreferrer" target="_blank"]] ===
5 +* ((( ==== **[[Intermediate >>||anchor = "HIntermediate-1"]]** ==== )))
8 8  
9 -//Level: advanced//
7 +* ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
10 10  
11 -=== [[Connectivity>>https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity||rel=" noopener noreferrer" target="_blank"]] ===
9 +=== **Beginner** ===
12 12  
13 -//Level: advanced//
11 +=== [[Starting a new study – Explore the anatomy>>https://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy||rel=" noopener noreferrer" target="_blank"]] ===
14 14  
15 -=== [[Connectivity Graphs>>https://neuroimage.usc.edu/brainstorm/Tutorials/ConnectivityGraph||rel=" noopener noreferrer" target="_blank"]] ===
13 +**Level**: beginner(%%) **Type**: interactive tutorial
16 16  
17 -//Level: advanced//
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.
16 +=== [[Starting a new study – Create a new protocol>>https://neuroimage.usc.edu/brainstorm/Tutorials/CreateProtocol||rel=" noopener noreferrer" target="_blank"]] ===
18 18  
19 -=== [[Converting to Brainstorm Events>>https://neuroimage.usc.edu/brainstorm/e-phys/ConvertToBrainstormEvents||rel=" noopener noreferrer" target="_blank"]] ===
18 +**Level**: beginner(%%) **Type**: interactive tutorial
20 20  
21 -//Level: advanced//
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.
22 +=== [[Brainstorm: Imaging neural activity at the speed of brain>>https://www.youtube.com/watch?v=30eFJUrRcN4||rel=" noopener noreferrer" target="_blank"]] ===
22 22  
23 -=== [[Coordinate systems>>https://neuroimage.usc.edu/brainstorm/CoordinateSystems||rel=" noopener noreferrer" target="_blank"]] ===
24 +**Level**: beginner(%%) **Type**: video tutorial
24 24  
25 -//Level: advanced//
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}}
30 +=== [[Starting a new study – Import the subject anatomy>>https://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy||rel=" noopener noreferrer" target="_blank"]] ===
26 26  
27 -=== [[Corticomuscular coherence (CTF MEG)>>https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence||rel=" noopener noreferrer" target="_blank"]] ===
32 +**Level**: beginner(%%) **Type**: interactive tutorial
28 28  
29 -//Level: advanced//
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.
35 +=== [[Introduction tutorials>>https://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction||rel=" noopener noreferrer" target="_blank"]] ===
30 30  
31 -=== [[Deriving LFP signals from raw signals>>https://neuroimage.usc.edu/brainstorm/e-phys/RawToLFP||rel=" noopener noreferrer" target="_blank"]] ===
37 +**Level**: beginner(%%) **Type**: -
32 32  
33 -//Level: advanced//
39 +=== **Intermediate** ===
34 34  
35 -=== [[Digitize EEG sensor locations and head shape>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutDigitize||rel=" noopener noreferrer" target="_blank"]] ===
41 +=== [[Reviewing – Event markers>>https://neuroimage.usc.edu/brainstorm/Tutorials/EventMarkers||rel=" noopener noreferrer" target="_blank"]] ===
36 36  
37 -//Level: advanced//
43 +**Level**: intermediate(%%) **Type**: interactive tutorial
38 38  
39 -=== [[ECoG/sEEG tutorial>>https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG||rel=" noopener noreferrer" target="_blank"]] ===
45 +=== [[Reviewing – Continuous recordings>>https://neuroimage.usc.edu/brainstorm/Tutorials/ReviewRaw||rel=" noopener noreferrer" target="_blank"]] ===
40 40  
41 -//Level: advanced//
47 +**Level**: intermediate(%%) **Type**: interactive tutorial
42 42  
43 -=== [[EEG and epilepsy>>https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy||rel=" noopener noreferrer" target="_blank"]] ===
49 +=== [[Reviewing – Multiple windows>>https://neuroimage.usc.edu/brainstorm/Tutorials/MultipleWindows||rel=" noopener noreferrer" target="_blank"]] ===
44 44  
45 -//Level: advanced//
51 +**Level**: intermediate(%%) **Type**: interactive tutorial
46 46  
47 -=== [[Elekta-Neuromag tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag||rel=" noopener noreferrer" target="_blank"]] ===
53 +=== [[Reviewing – Channel file / MRI registration>>https://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile||rel=" noopener noreferrer" target="_blank"]] ===
48 48  
49 -//Level: advanced//
55 +**Level**: intermediate(%%) **Type**: interactive tutorial
50 50  
51 -=== [[Epileptogenic Zone Fingerprint>>https://neuroimage.usc.edu/brainstorm/Tutorials/EZFingerprint||rel=" noopener noreferrer" target="_blank"]] ===
57 +=== **Advanced** ===
52 52  
53 -//Level: advanced//
54 -
55 -=== [[Export raw files in BIDS format>>https://neuroimage.usc.edu/brainstorm/ExportBids||rel=" noopener noreferrer" target="_blank"]] ===
56 -
57 -//Level: advanced//
58 -
59 59  === [[Export surface source maps to SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm12||rel=" noopener noreferrer" target="_blank"]] ===
60 60  
61 -//Level: advanced//
61 +**Level**: advanced(%%) **Type**: -
62 62  
63 -=== [[Export volume source maps to SPM8 / SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm8||rel=" noopener noreferrer" target="_blank"]] ===
63 +=== [[MEG current phantom (Elekta-Neuromag)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomElekta||rel=" noopener noreferrer" target="_blank"]] ===
64 64  
65 -//Level: advanced//
65 +**Level**: advanced(%%) **Type**: -
66 66  
67 -=== [[FEM advanced tutorial with MEG/EEG Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMedianNerve||rel=" noopener noreferrer" target="_blank"]] ===
67 +=== [[Plugins>>https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins||rel=" noopener noreferrer" target="_blank"]] ===
68 68  
69 -//Level: advanced//
69 +**Level**: advanced(%%) **Type**: -
70 70  
71 71  === [[FEM mesh generation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMesh||rel=" noopener noreferrer" target="_blank"]] ===
72 72  
73 -//Level: advanced//
73 +**Level**: advanced(%%) **Type**: -
74 74  
75 -=== [[FEM tensors estimation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemTensors||rel=" noopener noreferrer" target="_blank"]] ===
75 +=== [[Group analysis: Subject coregistration>>https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects||rel=" noopener noreferrer" target="_blank"]] ===
76 76  
77 -//Level: advanced//
77 +**Level**: advanced(%%) **Type**: -
78 78  
79 -=== [[Fitting dipoles with FieldTrip>>https://neuroimage.usc.edu/brainstorm/Tutorials/DipoleFitting||rel=" noopener noreferrer" target="_blank"]] ===
79 +=== [[FEM advanced tutorial with MEG/EEG Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMedianNerve||rel=" noopener noreferrer" target="_blank"]] ===
80 80  
81 -//Level: advanced//
81 +**Level**: advanced(%%) **Type**: -
82 82  
83 -=== [[Fitting Oscillations and One-Over-F (FOOOF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/Fooof||rel=" noopener noreferrer" target="_blank"]] ===
83 +=== [[Connectivity>>https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity||rel=" noopener noreferrer" target="_blank"]] ===
84 84  
85 -//Level: advanced//
85 +**Level**: advanced(%%) **Type**: -
86 86  
87 -=== [[Functions for Basic e-phys>>https://neuroimage.usc.edu/brainstorm/e-phys/functions||rel=" noopener noreferrer" target="_blank"]] ===
87 +=== [[Corticomuscular coherence (CTF MEG)>>https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence||rel=" noopener noreferrer" target="_blank"]] ===
88 88  
89 -//Level: advanced//
89 +**Level**: advanced(%%) **Type**: -
90 90  
91 -=== [[Granger causality>>https://neuroimage.usc.edu/brainstorm/GrangerCausality||rel=" noopener noreferrer" target="_blank"]] ===
91 +=== [[Best: Brain Entropy in space and time>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutBEst||rel=" noopener noreferrer" target="_blank"]] ===
92 92  
93 -//Level: advanced//
93 +**Level**: advanced(%%) **Type**: -
94 94  
95 -=== [[Group analysis: Subject coregistration>>https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects||rel=" noopener noreferrer" target="_blank"]] ===
95 +=== [[Epileptogenic Zone Fingerprint>>https://neuroimage.usc.edu/brainstorm/Tutorials/EZFingerprint||rel=" noopener noreferrer" target="_blank"]] ===
96 96  
97 -//Level: advanced//
97 +**Level**: advanced(%%) **Type**: -
98 98  
99 -=== [[How to write your own process>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutUserProcess||rel=" noopener noreferrer" target="_blank"]] ===
99 +=== [[SSP Cookbook>>https://neuroimage.usc.edu/brainstorm/Tutorials/SSPCookbook||rel=" noopener noreferrer" target="_blank"]] ===
100 100  
101 -//Level: advanced//
101 +**Level**: advanced(%%) **Type**: -
102 102  
103 -=== [[Human Connectome Project: Resting-state MEG>>https://neuroimage.usc.edu/brainstorm/Tutorials/HCP-MEG||rel=" noopener noreferrer" target="_blank"]] ===
103 +=== [[Elekta-Neuromag tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag||rel=" noopener noreferrer" target="_blank"]] ===
104 104  
105 -//Level: advanced//
105 +**Level**: advanced(%%) **Type**: -
106 106  
107 -=== [[MEG current phantom (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomCtf||rel=" noopener noreferrer" target="_blank"]] ===
107 +=== [[Using BrainVISA>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainVisa||rel=" noopener noreferrer" target="_blank"]] ===
108 108  
109 -//Level: advanced//
109 +**Level**: advanced(%%) **Type**: -
110 110  
111 -=== [[MEG current phantom (Elekta-Neuromag)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomElekta||rel=" noopener noreferrer" target="_blank"]] ===
112 -
113 -//Level: advanced//
114 -
115 115  === [[MEG median nerve tutorial (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/MedianNerveCtf||rel=" noopener noreferrer" target="_blank"]] ===
116 116  
117 -//Level: advanced//
113 +**Level**: advanced(%%) **Type**: -
118 118  
119 -=== [[MEG visual tutorial: Group analysis (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup||rel=" noopener noreferrer" target="_blank"]] ===
115 +=== [[Spike Sorting in Brainstorm>>https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting||rel=" noopener noreferrer" target="_blank"]] ===
120 120  
121 -//Level: advanced//
117 +**Level**: advanced(%%) **Type**: -
122 122  
123 -=== [[MEG visual tutorial: Single subject (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle||rel=" noopener noreferrer" target="_blank"]] ===
119 +=== [[Coordinate systems>>https://neuroimage.usc.edu/brainstorm/CoordinateSystems||rel=" noopener noreferrer" target="_blank"]] ===
124 124  
125 -//Level: advanced//
121 +**Level**: advanced(%%) **Type**: -
126 126  
127 -=== [[Montage editor>>https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor||rel=" noopener noreferrer" target="_blank"]] ===
123 +=== [[Real-time head-tracking for adjusting head position>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime||rel=" noopener noreferrer" target="_blank"]] ===
128 128  
129 -//Level: advanced//
125 +**Level**: advanced(%%) **Type**: -
130 130  
131 -=== [[MRI Segmentation with CAT12>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12||rel=" noopener noreferrer" target="_blank"]] ===
127 +=== [[Spectral Parameterization Resolved in Time (SPRiNT)>>https://neuroimage.usc.edu/brainstorm/Tutorials/SPRiNT||rel=" noopener noreferrer" target="_blank"]] ===
132 132  
133 -//Level: advanced//
129 +**Level**: advanced(%%) **Type**: -
134 134  
135 -=== [[MRI segmentation with CIVET>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCIVET||rel=" noopener noreferrer" target="_blank"]] ===
131 +=== [[Montage editor>>https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor||rel=" noopener noreferrer" target="_blank"]] ===
136 136  
137 -//Level: advanced//
133 +**Level**: advanced(%%) **Type**: -
138 138  
139 -=== [[MRI segmentation with FastSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegFastSurfer||rel=" noopener noreferrer" target="_blank"]] ===
135 +=== [[Tutorial - Head Motion>>https://neuroimage.usc.edu/brainstorm/Tutorials/HeadMotion||rel=" noopener noreferrer" target="_blank"]] ===
140 140  
141 -//Level: advanced//
137 +**Level**: advanced(%%) **Type**: -
142 142  
143 -=== [[NIRS data importation, visualization and response estimate in the optode space>>https://neuroimage.usc.edu/brainstorm/Tutorials/NIRSFingerTapping||rel=" noopener noreferrer" target="_blank"]] ===
139 +=== [[Virtual Fiber Tracks for Connectivity Visualization>>https://neuroimage.usc.edu/brainstorm/Tutorials/FiberConnectivity||rel=" noopener noreferrer" target="_blank"]] ===
144 144  
145 -//Level: advanced//
141 +**Level**: advanced(%%) **Type**: -
146 146  
147 -=== [[Plugins>>https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins||rel=" noopener noreferrer" target="_blank"]] ===
143 +=== [[MEG visual tutorial: Single subject (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle||rel=" noopener noreferrer" target="_blank"]] ===
148 148  
149 -//Level: advanced//
145 +**Level**: advanced(%%) **Type**: -
150 150  
151 -=== [[Real-time head-tracking for adjusting head position>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime||rel=" noopener noreferrer" target="_blank"]] ===
147 +=== [[Digitize EEG sensor locations and head shape>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutDigitize||rel=" noopener noreferrer" target="_blank"]] ===
152 152  
153 -//Level: advanced//
149 +**Level**: advanced(%%) **Type**: -
154 154  
155 -=== [[Realistic head model: FEM with DUNEuro>>https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro||rel=" noopener noreferrer" target="_blank"]] ===
151 +=== [[MEG visual tutorial: Group analysis (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup||rel=" noopener noreferrer" target="_blank"]] ===
156 156  
157 -//Level: advanced//
153 +**Level**: advanced(%%) **Type**: -
158 158  
159 -=== [[Resting state recordings from the OMEGA database>>https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega||rel=" noopener noreferrer" target="_blank"]] ===
155 +=== [[Converting to Brainstorm Events>>https://neuroimage.usc.edu/brainstorm/e-phys/ConvertToBrainstormEvents||rel=" noopener noreferrer" target="_blank"]] ===
160 160  
161 -//Level: advanced//
157 +**Level**: advanced(%%) **Type**: -
162 162  
163 -=== [[Simulations>>https://neuroimage.usc.edu/brainstorm/Tutorials/Simulations||rel=" noopener noreferrer" target="_blank"]] ===
164 -
165 -//Level: advanced//
166 -
167 -=== [[Spectral Parameterization Resolved in Time (SPRiNT)>>https://neuroimage.usc.edu/brainstorm/Tutorials/SPRiNT||rel=" noopener noreferrer" target="_blank"]] ===
168 -
169 -//Level: advanced//
170 -
171 -=== [[Spike Sorting in Brainstorm>>https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting||rel=" noopener noreferrer" target="_blank"]] ===
172 -
173 -//Level: advanced//
174 -
175 -=== [[SSP Cookbook>>https://neuroimage.usc.edu/brainstorm/Tutorials/SSPCookbook||rel=" noopener noreferrer" target="_blank"]] ===
176 -
177 -//Level: advanced//
178 -
179 179  === [[Synchronization with eye tracker (event transfer)>>https://neuroimage.usc.edu/brainstorm/Tutorials/EyetrackSynchro||rel=" noopener noreferrer" target="_blank"]] ===
180 180  
181 -//Level: advanced//
161 +**Level**: advanced(%%) **Type**: -
182 182  
183 -=== [[T1-MRI Segmentation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite||rel=" noopener noreferrer" target="_blank"]] ===
163 +=== [[Using the anatomy templates>>https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy||rel=" noopener noreferrer" target="_blank"]] ===
184 184  
185 -//Level: advanced//
165 +**Level**: advanced(%%) **Type**: -
186 186  
187 -=== [[Tutorial - Head Motion>>https://neuroimage.usc.edu/brainstorm/Tutorials/HeadMotion||rel=" noopener noreferrer" target="_blank"]] ===
167 +=== [[Fitting dipoles with FieldTrip>>https://neuroimage.usc.edu/brainstorm/Tutorials/DipoleFitting||rel=" noopener noreferrer" target="_blank"]] ===
188 188  
189 -//Level: advanced//
169 +**Level**: advanced(%%) **Type**: -
190 190  
191 -=== [[Using BrainVISA>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainVisa||rel=" noopener noreferrer" target="_blank"]] ===
171 +=== [[Deriving LFP signals from raw signals>>https://neuroimage.usc.edu/brainstorm/e-phys/RawToLFP||rel=" noopener noreferrer" target="_blank"]] ===
192 192  
193 -//Level: advanced//
173 +**Level**: advanced(%%) **Type**: -
194 194  
195 -=== [[Using FreeSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer||rel=" noopener noreferrer" target="_blank"]] ===
175 +=== [[MEG current phantom (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomCtf||rel=" noopener noreferrer" target="_blank"]] ===
196 196  
197 -//Level: advanced//
177 +**Level**: advanced(%%) **Type**: -
198 198  
199 -=== [[Using the anatomy templates>>https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy||rel=" noopener noreferrer" target="_blank"]] ===
200 200  
201 -//Level: advanced//
202 -
203 -=== [[Virtual Fiber Tracks for Connectivity Visualization>>https://neuroimage.usc.edu/brainstorm/Tutorials/FiberConnectivity||rel=" noopener noreferrer" target="_blank"]] ===
204 -
205 -//Level: advanced//
206 -
207 -=== [[Yokogawa/KIT tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/Yokogawa||rel=" noopener noreferrer" target="_blank"]] ===
208 -
209 -//Level: advanced//
210 -
211 -