Last modified by fousekjan on 2022/05/23 22:36
From version 4.1
edited by fousekjan
on 2020/06/12 17:42
Change comment: There is no comment for this version
To version 11.2
edited by fousekjan
on 2020/06/13 18:26
Change comment: Added tag [tvb, the virtual brain]

Summary

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1 +tvb|the virtual brain
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= My Collab's Extended Title =
5 += TVB resting state dataset =
6 6  
7 -My collab's subtitle
7 +Synthetic resting state recordings of simultaneous fMRI + EEG
8 8  )))
9 9  )))
10 10  
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12 12  (((
13 13  (% class="col-xs-12 col-sm-8" %)
14 14  (((
15 -= What can I find here? =
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  
17 -* Notice how the table of contents on the right
18 -* is automatically updated
19 -* to hold this page's headers
17 +== Parcellation and Structural Connectivity ==
20 20  
21 -= Who has access? =
19 +{{code}}
20 +sub-<label>/connectivity/
21 +├── sub-<label>_atlas-dk_conndata-network_connectivity.json
22 +├── sub-<label>_atlas-dk_desc-distance_conndata-network_connectivity.tsv
23 +└── sub-<label>_atlas-dk_desc-weight_conndata-network_connectivity.tsv
24 +{{/code}}
22 22  
23 -Describe the audience of this collab.
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**.
27 +
28 +(% style="text-align:center" %)
29 +[[image:sub-001_connectome.png||alt="connectome"]]
30 +
31 +== BOLD fMRI ==
32 +
33 +{{code}}
34 +sub-<label>/func/
35 +├── sub-<label>_task-rest_atlas-dk_desc-sim_timeseries.json
36 +└── sub-<label>_task-rest_atlas-dk_desc-sim_timeseries.tsv.gz
37 +{{/code}}
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.
40 +
41 +(% style="text-align:center" %)
42 +[[image:sub-001_bold_with_fc.png||alt="bold"]]
43 +
44 +== EEG ==
45 +
46 +{{code}}
47 +sub-<label>/eeg
48 +├── sub-<label>_task-rest_desc-sim_coordsystem.json
49 +├── sub-<label>_task-rest_desc-sim_eeg.eeg
50 +├── sub-<label>_task-rest_desc-sim_eeg.json
51 +├── sub-<label>_task-rest_desc-sim_eeg.vhdr
52 +├── sub-<label>_task-rest_desc-sim_eeg.vmrk
53 +└── sub-<label>_task-rest_desc-sim_electrodes.tsv
54 +{{/code}}
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.
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 +== References ==
67 +
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.
69 +
70 +
71 +
24 24  )))
25 25  
26 26  
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