Wiki source code of TVB synthetic resting state dataset

Last modified by fousekjan on 2022/05/23 22:36

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10.1	5	= TVB resting state dataset =
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10.1	7	Synthetic resting state recordings of simultaneous fMRI + EEG
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15.3	15	This dataset contains 10 minutes of resting state fMRI and EEG time series simulated with brain network model (Sanz-Leon et al., 2015, 2013) implemented in [[The Virtual Brain>>url:https://www.thevirtualbrain.org/]]. More precise information on the model used to generate these data is deliberately not provided here. The data will be available for a period of time without the model description to get unbiased feedback from the community analyzing empirical data. The model description will be published in a separate document.
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4.2	17	== Parcellation and Structural Connectivity ==
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	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}}
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10.1	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.
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	29	[[image:sub-001_connectome.png\|\|alt="connectome"]]
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4.2	31	== BOLD fMRI ==
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	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}}
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10.1	39	The simulated BOLD (TR=2) time series for the ROIs is stored as compressed .tsv file with columns defined in the json sidecar.
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	42	[[image:sub-001_bold_with_fc.png\|\|alt="bold"]]
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4.2	44	== EEG ==
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10.1	46	{{code}}
	47	sub-<label>/eeg
4.2	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
10.1	53	└── sub-<label>_task-rest_desc-sim_electrodes.tsv
	54	{{/code}}
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10.1	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.
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	59	[[image:sub-001_eeg_traces.png\|\|alt="eeg traces"]]
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	62	[[image:sub-002_eeg_psd.png\|\|alt="eeg psd"]]
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	64	== [[image:sub-002_sensors.png\|\|alt="eeg sensors"]] ==
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4.2	66	== References ==
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15.2	68	Desikan, R. S., Ségonne, F., Fischl, B., Quinn, B. T., Dickerson, B. C., Blacker, D., Buckner, R. L., Dale, A. M., Maguire, R. P., Hyman, B. T., Albert, M. S., & Killiany, R. J. (2006). An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. NeuroImage, 31(3), 968–980.
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15.3	70	Sanz-Leon, P., Knock, S. A., Woodman, M. M., Domide, L., Mersmann, J., McIntosh, A. R., & Jirsa, V. (2013). The Virtual Brain: a simulator of primate brain network dynamics. Frontiers in neuroinformatics, 7.
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15.2	72	Sanz-Leon, P., Knock, S. A., Spiegler, A., & Jirsa, V. K. (2015). Mathematical framework for large-scale brain network modeling in The Virtual Brain. NeuroImage, 111, 385–430.
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	77	{{box title="Contents"}}
	78	{{toc/}}
	79	{{/box}}
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