Last modified by fousekjan on 2022/05/23 22:36
From version 11.2
edited by fousekjan
on 2020/06/13 18:26
Change comment: Added tag [tvb, the virtual brain]
To version 9.1
edited by fousekjan
on 2020/06/13 18:09
Change comment: Uploaded new attachment "sub-002_sensors.png", version {1}

Summary

Details

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1 -tvb|the virtual brain
Content
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= TVB resting state dataset =
5 += My Collab's Extended Title =
6 6  
7 -Synthetic resting state recordings of simultaneous fMRI + EEG
7 +My collab's subtitle
8 8  )))
9 9  )))
10 10  
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12 12  (((
13 13  (% class="col-xs-12 col-sm-8" %)
14 14  (((
15 += =
16 +
17 += Synthetic resting state fMRI + EEG =
18 +
15 15  This dataset contains 10 minutes of resting state fMRI and EEG time series simulated with a brain network model implemented in [[The Virtual Brain>>url:https://www.thevirtualbrain.org/]]. More precise information in the model used to generate these data is deliberately not provided here. It will be published in a separate document.
16 16  
21 +
17 17  == Parcellation and Structural Connectivity ==
18 18  
19 19  {{code}}
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23 23  └── sub-<label>_atlas-dk_desc-weight_conndata-network_connectivity.tsv
24 24  {{/code}}
25 25  
26 -The structural connectivity is stored in two separate .tsv files containing the weights (au) and tract lengths (mm) matrices ordered as sources x targets. The 84 regions are defined by the FreeSurfer parcellation by Desikan-Killiany Atlas (Desikan et al, 2006). Mapping of region labels to names is defined in **dk_atlas.tsv**.
31 +The structural connectivity is stored in two separate .tsv files containing the weights (au) and tract lengths (mm) matrices ordered as sources x targets. The 84 regions are defined by the FreeSurfer parcellation by Desikan-Killiany Atlas (Desikan et al, 2006). Mapping of region labels to names is defined in dk_atlas.tsv.
27 27  
28 -(% style="text-align:center" %)
29 -[[image:sub-001_connectome.png||alt="connectome"]]
30 -
31 31  == BOLD fMRI ==
32 32  
33 33  {{code}}
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36 36  └── sub-<label>_task-rest_atlas-dk_desc-sim_timeseries.tsv.gz
37 37  {{/code}}
38 38  
39 -The simulated BOLD (TR=2) time series for the ROIs is stored as compressed **.tsv** file with columns defined in the json sidecar.
41 +The simulated BOLD (TR=2) time series for the ROIs is stored as compressed .tsv file with columns defined in the json sidecar.
40 40  
41 -(% style="text-align:center" %)
42 -[[image:sub-001_bold_with_fc.png||alt="bold"]]
43 -
44 44  == EEG ==
45 45  
46 -{{code}}
47 -sub-<label>/eeg
45 +{{{sub-<label>/eeg
48 48  ├── sub-<label>_task-rest_desc-sim_coordsystem.json
49 49  ├── sub-<label>_task-rest_desc-sim_eeg.eeg
50 50  ├── sub-<label>_task-rest_desc-sim_eeg.json
51 51  ├── sub-<label>_task-rest_desc-sim_eeg.vhdr
52 52  ├── sub-<label>_task-rest_desc-sim_eeg.vmrk
53 -└── sub-<label>_task-rest_desc-sim_electrodes.tsv
54 -{{/code}}
51 +└── sub-<label>_task-rest_desc-sim_electrodes.tsv}}}
55 55  
56 -The EEG was simulated using a montage for HydroCel Geodesic Sensor Net with 256 electrodes. The raw data sampled at 256Hz was only high-pass filtered (FIR window length 845 samples, 1Hz cutoff), and stored in the [[BrainVision triplet format>>url:https://mne.tools/stable/generated/mne.io.read_raw_brainvision.html]] (**.eeg**, **.vmrk**, **.vhdr**). The electrode labels and locations are listed in the ***_electrodes.tsv** file.
53 +The EEG was simulated using a montage for HydroCel Geodesic Sensor Net with 256 electrodes. The raw data sampled at 256Hz was only high-pass filtered (FIR window length 845 samples, 1Hz cutoff), and stored in the [[BrainVision triplet format>>url:https://mne.tools/stable/generated/mne.io.read_raw_brainvision.html]] (.eeg, .vmrk, .vhdr). The electrode labels and locations are listed in the *_electrodes.tsv file.
57 57  
58 -(% style="text-align:center" %)
59 -[[image:sub-001_eeg_traces.png||alt="eeg traces"]]
60 -
61 -(% style="text-align:center" %)
62 -[[image:sub-002_eeg_psd.png||alt="eeg psd"]]
63 -
64 -== [[image:sub-002_sensors.png||alt="eeg sensors"]] ==
65 -
66 66  == References ==
67 67  
68 68  Desikan RS, Segonne F, Fischl B, Quinn BT, Dickerson BC, Blacker D, Buckner RL, Dale AM, Maguire RP, Hyman BT, Albert MS, Killiany RJ. An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. Neuroimage. 2006;31:968–980.