Changes for page Tools and services tutorials
Last modified by abonard on 2025/05/23 13:23
From version 19.1
edited by adavison
on 2023/02/27 14:03
on 2023/02/27 14:03
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To version 17.1
edited by annedevismes
on 2023/02/23 11:10
on 2023/02/23 11:10
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... ... @@ -1,10 +1,11 @@ 1 -(% class="box infomessage" id="HWelcometothesingleentrypointtotutorialsforEBRAINStoolsandservices.Here2CyoucanfindalistofEBRAINSofferings2Csortedbytopic2Candlinkstotheirtutorials." style="text-align: center;" %) 2 -((( 3 -Welcome to the single entry point to tutorials for EBRAINS tools and services. Here, you can find a list of EBRAINS offerings, sorted by topic, and links to their tutorials. 4 -))) 1 +(% style="text-align: center;" %) 2 +=== Welcome to the single entry point to tutorials for EBRAINS tools and services. Here, you can find a list of EBRAINS offerings, sorted by topic, and links to their tutorials. === 5 5 6 -Some of the tutorials can also be accessed via the [[EBRAINS YouTube channel>>https://www.youtube.com/channel/UC6E796cVVR5Xrs2A5jJmleQ]]. 7 7 5 +This page is work in progress. It is incomplete for now. But it will include all of EBRAINS tutorials very soon. 6 + 7 +Some tutorials are also available on [[EBRAINS YouTube channel>>https://www.youtube.com/channel/UC6E796cVVR5Xrs2A5jJmleQ]]. 8 + 8 8 == Arbor == 9 9 10 10 * [[A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel="noopener noreferrer" target="_blank"]] (beginner) ... ... @@ -21,73 +21,6 @@ 21 21 * [[Spike Timing-dependent Plasticity Curve>>https://docs.arbor-sim.org/en/stable/tutorial/calcium_stdp_curve.html||rel="noopener noreferrer" target="_blank"]] (advanced) 22 22 * [[Two cells connected via a gap junction>>https://docs.arbor-sim.org/en/stable/tutorial/network_two_cells_gap_junctions.html||rel="noopener noreferrer" target="_blank"]] (advanced) 23 23 24 -== Bids Manager & Pipeline == 25 - 26 -* [[BIDS Manager>>https://github.com/Dynamap/BIDS_Manager/blob/master/Tutorial_BIDS_Manager.pdf||rel="noopener noreferrer" target="_blank"]] (advanced) 27 - 28 -== BluePyMM == 29 - 30 -* [[BluePyMM>>https://github.com/BlueBrain/BluePyMM/blob/master/notebook/BluePyMM.ipynb||rel="noopener noreferrer" target="_blank"]] (beginner) 31 - 32 -== BluePyOpt == 33 - 34 -* [[Creating a simple cell optimisation>>https://github.com/BlueBrain/BluePyOpt/blob/master/examples/simplecell/simplecell.ipynb||rel="noopener noreferrer" target="_blank"]] (beginner) 35 - 36 -== Brainstorm == 37 - 38 -* [[Introduction tutorials>>https://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction||rel="noopener noreferrer" target="_blank"]] (beginner) 39 -* [[Best: Brain Entropy in space and time>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutBEst||rel="noopener noreferrer" target="_blank"]] (advanced) 40 -* [[Connectivity>>https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity||rel="noopener noreferrer" target="_blank"]] (advanced) 41 -* [[Connectivity Graphs>>https://neuroimage.usc.edu/brainstorm/Tutorials/ConnectivityGraph||rel="noopener noreferrer" target="_blank"]] (advanced) 42 -* [[Converting to Brainstorm Events>>https://neuroimage.usc.edu/brainstorm/e-phys/ConvertToBrainstormEvents||rel="noopener noreferrer" target="_blank"]] (advanced) 43 -* [[Coordinate systems>>https://neuroimage.usc.edu/brainstorm/CoordinateSystems||rel="noopener noreferrer" target="_blank"]] (advanced) 44 -* [[Corticomuscular coherence (CTF MEG)>>https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence||rel="noopener noreferrer" target="_blank"]] (advanced) 45 -* [[Deriving LFP signals from raw signals>>https://neuroimage.usc.edu/brainstorm/e-phys/RawToLFP||rel="noopener noreferrer" target="_blank"]] (advanced) 46 -* [[Digitize EEG sensor locations and head shape>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutDigitize||rel="noopener noreferrer" target="_blank"]] (advanced) 47 -* [[ECoG/sEEG tutorial>>https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG||rel="noopener noreferrer" target="_blank"]] (advanced) 48 -* [[EEG and epilepsy>>https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy||rel="noopener noreferrer" target="_blank"]] (advanced) 49 -* [[Elekta-Neuromag tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag||rel="noopener noreferrer" target="_blank"]] (advanced) 50 -* [[Epileptogenic Zone Fingerprint>>https://neuroimage.usc.edu/brainstorm/Tutorials/EZFingerprint||rel="noopener noreferrer" target="_blank"]] (advanced) 51 -* [[Export raw files in BIDS format>>https://neuroimage.usc.edu/brainstorm/ExportBids||rel="noopener noreferrer" target="_blank"]] (advanced) 52 -* [[Export surface source maps to SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm12||rel="noopener noreferrer" target="_blank"]] (advanced) 53 -* [[Export volume source maps to SPM8 / SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm8||rel="noopener noreferrer" target="_blank"]] (advanced) 54 -* [[FEM advanced tutorial with MEG/EEG Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMedianNerve||rel="noopener noreferrer" target="_blank"]] (advanced) 55 -* [[FEM mesh generation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMesh||rel="noopener noreferrer" target="_blank"]] (advanced) 56 -* [[FEM tensors estimation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemTensors||rel="noopener noreferrer" target="_blank"]] (advanced) 57 -* [[Fitting dipoles with FieldTrip>>https://neuroimage.usc.edu/brainstorm/Tutorials/DipoleFitting||rel="noopener noreferrer" target="_blank"]] (advanced) 58 -* [[Fitting Oscillations and One-Over-F (FOOOF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/Fooof||rel="noopener noreferrer" target="_blank"]] (advanced) 59 -* [[Functions for Basic e-phys>>https://neuroimage.usc.edu/brainstorm/e-phys/functions||rel="noopener noreferrer" target="_blank"]] (advanced) 60 -* [[Granger causality>>https://neuroimage.usc.edu/brainstorm/GrangerCausality||rel="noopener noreferrer" target="_blank"]] (advanced) 61 -* [[Group analysis: Subject coregistration>>https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects||rel="noopener noreferrer" target="_blank"]] (advanced) 62 -* [[How to write your own process>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutUserProcess||rel="noopener noreferrer" target="_blank"]] (advanced) 63 -* [[Human Connectome Project: Resting-state MEG>>https://neuroimage.usc.edu/brainstorm/Tutorials/HCP-MEG||rel="noopener noreferrer" target="_blank"]] (advanced) 64 -* [[MEG current phantom (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomCtf||rel="noopener noreferrer" target="_blank"]] (advanced) 65 -* [[MEG current phantom (Elekta-Neuromag)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomElekta||rel="noopener noreferrer" target="_blank"]] (advanced) 66 -* [[MEG median nerve tutorial (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/MedianNerveCtf||rel="noopener noreferrer" target="_blank"]] (advanced) 67 -* [[MEG visual tutorial: Group analysis (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup||rel="noopener noreferrer" target="_blank"]] (advanced) 68 -* [[MEG visual tutorial: Single subject (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle||rel="noopener noreferrer" target="_blank"]] (advanced) 69 -* [[Montage editor>>https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor||rel="noopener noreferrer" target="_blank"]] (advanced) 70 -* [[MRI Segmentation with CAT12>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12||rel="noopener noreferrer" target="_blank"]] (advanced) 71 -* [[MRI segmentation with CIVET>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCIVET||rel="noopener noreferrer" target="_blank"]] (advanced) 72 -* [[MRI segmentation with FastSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegFastSurfer||rel="noopener noreferrer" target="_blank"]] (advanced) 73 -* [[NIRS data importation, visualization and response estimate in the optode space>>https://neuroimage.usc.edu/brainstorm/Tutorials/NIRSFingerTapping||rel="noopener noreferrer" target="_blank"]] (advanced) 74 -* [[Plugins>>https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins||rel="noopener noreferrer" target="_blank"]] (advanced) 75 -* [[Real-time head-tracking for adjusting head position>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime||rel="noopener noreferrer" target="_blank"]] (advanced) 76 -* [[Realistic head model: FEM with DUNEuro>>https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro||rel="noopener noreferrer" target="_blank"]] (advanced) 77 -* [[Resting state recordings from the OMEGA database>>https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega||rel="noopener noreferrer" target="_blank"]] (advanced) 78 -* [[Simulations>>https://neuroimage.usc.edu/brainstorm/Tutorials/Simulations||rel="noopener noreferrer" target="_blank"]] (advanced) 79 -* [[Spectral Parameterization Resolved in Time (SPRiNT)>>https://neuroimage.usc.edu/brainstorm/Tutorials/SPRiNT||rel="noopener noreferrer" target="_blank"]] (advanced) 80 -* [[Spike Sorting in Brainstorm>>https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting||rel="noopener noreferrer" target="_blank"]] (advanced) 81 -* [[SSP Cookbook>>https://neuroimage.usc.edu/brainstorm/Tutorials/SSPCookbook||rel="noopener noreferrer" target="_blank"]] (advanced) 82 -* [[Synchronization with eye tracker (event transfer)>>https://neuroimage.usc.edu/brainstorm/Tutorials/EyetrackSynchro||rel="noopener noreferrer" target="_blank"]] (advanced) 83 -* [[T1-MRI Segmentation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite||rel="noopener noreferrer" target="_blank"]] (advanced) 84 -* [[Tutorial - Head Motion>>https://neuroimage.usc.edu/brainstorm/Tutorials/HeadMotion||rel="noopener noreferrer" target="_blank"]] (advanced) 85 -* [[Using BrainVISA>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainVisa||rel="noopener noreferrer" target="_blank"]] (advanced) 86 -* [[Using FreeSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer||rel="noopener noreferrer" target="_blank"]] (advanced) 87 -* [[Using the anatomy templates>>https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy||rel="noopener noreferrer" target="_blank"]] (advanced) 88 -* [[Virtual Fiber Tracks for Connectivity Visualization>>https://neuroimage.usc.edu/brainstorm/Tutorials/FiberConnectivity||rel="noopener noreferrer" target="_blank"]] (advanced) 89 -* [[Yokogawa/KIT tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/Yokogawa||rel="noopener noreferrer" target="_blank"]] (advanced) 90 - 91 91 == Electrophysiology Analysis Toolkit == 92 92 93 93 * [[Statistics of spike trains>>https://elephant.readthedocs.io/en/latest/tutorials/statistics.html||rel="noopener noreferrer" target="_blank"]] (beginner) ... ... @@ -98,10 +98,6 @@ 98 98 * [[The Unitary Events Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/unitary_event_analysis.html||rel="noopener noreferrer" target="_blank"]] (advanced) 99 99 * [[Time-domain Granger Causality>>https://elephant.readthedocs.io/en/latest/tutorials/granger_causality.html||rel="noopener noreferrer" target="_blank"]] (advanced) 100 100 101 -== Hodgkin Huxley Neuron Builder == 102 - 103 -* [[Hodgkin-Huxley Neuron Builder>>https://object.cscs.ch/v1/AUTH_c0a333ecf7c045809321ce9d9ecdfdea/web-resources-bsp/bsp-video-tutorials/HodgkinHuxleyNeuronBuilder/index.html||rel="noopener noreferrer" target="_blank"]] (advanced) 104 - 105 105 == NEST == 106 106 107 107 * [[Introduction to NEST: Simulating a single neuron>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/videos/one_neuron.html||rel="noopener noreferrer" target="_blank"]] (beginner)