Last modified by fousekjan on 2022/05/23 22:36
From version 10.1
edited by fousekjan
on 2020/06/13 18:09
Change comment: There is no comment for this version
To version 1.1
edited by fousekjan
on 2020/06/12 17:42
Change comment: Collab created through API

Summary

Details

Page properties
Content
... ... @@ -2,9 +2,9 @@
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  
... ... @@ -12,65 +12,15 @@
12 12  (((
13 13  (% class="col-xs-12 col-sm-8" %)
14 14  (((
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.
15 += What can I find here? =
16 16  
17 +* Notice how the table of contents on the right
18 +* is automatically updated
19 +* to hold this page's headers
17 17  
18 -== Parcellation and Structural Connectivity ==
21 += Who has access? =
19 19  
20 -{{code}}
21 -sub-<label>/connectivity/
22 -├── sub-<label>_atlas-dk_conndata-network_connectivity.json
23 -├── sub-<label>_atlas-dk_desc-distance_conndata-network_connectivity.tsv
24 -└── sub-<label>_atlas-dk_desc-weight_conndata-network_connectivity.tsv
25 -{{/code}}
26 -
27 -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**.
28 -
29 -(% style="text-align:center" %)
30 -[[image:sub-001_connectome.png||alt="connectome"]]
31 -
32 -== BOLD fMRI ==
33 -
34 -{{code}}
35 -sub-<label>/func/
36 -├── sub-<label>_task-rest_atlas-dk_desc-sim_timeseries.json
37 -└── sub-<label>_task-rest_atlas-dk_desc-sim_timeseries.tsv.gz
38 -{{/code}}
39 -
40 -The simulated BOLD (TR=2) time series for the ROIs is stored as compressed **.tsv** file with columns defined in the json sidecar.
41 -
42 -(% style="text-align:center" %)
43 -[[image:sub-001_bold_with_fc.png||alt="bold"]]
44 -
45 -== EEG ==
46 -
47 -{{code}}
48 -sub-<label>/eeg
49 -├── sub-<label>_task-rest_desc-sim_coordsystem.json
50 -├── sub-<label>_task-rest_desc-sim_eeg.eeg
51 -├── sub-<label>_task-rest_desc-sim_eeg.json
52 -├── sub-<label>_task-rest_desc-sim_eeg.vhdr
53 -├── sub-<label>_task-rest_desc-sim_eeg.vmrk
54 -└── sub-<label>_task-rest_desc-sim_electrodes.tsv
55 -{{/code}}
56 -
57 -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.
58 -
59 -(% style="text-align:center" %)
60 -[[image:sub-001_eeg_traces.png||alt="eeg traces"]]
61 -
62 -(% style="text-align:center" %)
63 -[[image:sub-002_eeg_psd.png||alt="eeg psd"]]
64 -
65 -(% class="wikigeneratedid" %)
66 -== [[image:sub-002_sensors.png||alt="eeg sensors"]] ==
67 -
68 -== References ==
69 -
70 -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.
71 -
72 -
73 -
23 +Describe the audience of this collab.
74 74  )))
75 75  
76 76  
sub-001_bold_with_fc.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.fousekjan
Size
... ... @@ -1,1 +1,0 @@
1 -238.7 KB
Content
sub-001_connectome.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.fousekjan
Size
... ... @@ -1,1 +1,0 @@
1 -380.5 KB
Content
sub-001_eeg_traces.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.fousekjan
Size
... ... @@ -1,1 +1,0 @@
1 -372.5 KB
Content
sub-002_eeg_psd.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.fousekjan
Size
... ... @@ -1,1 +1,0 @@
1 -76.4 KB
Content
sub-002_sensors.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.fousekjan
Size
... ... @@ -1,1 +1,0 @@
1 -568.8 KB
Content
XWiki.XWikiRights[0]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Groups
... ... @@ -1,1 +1,0 @@
1 -Collabs.tvb-synthetic-resting-state-dataset._.groups.collab-tvb-synthetic-resting-state-dataset-viewer
Levels
... ... @@ -1,1 +1,0 @@
1 -view,comment
XWiki.XWikiRights[1]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Groups
... ... @@ -1,1 +1,0 @@
1 -Collabs.tvb-synthetic-resting-state-dataset._.groups.collab-tvb-synthetic-resting-state-dataset-editor
Levels
... ... @@ -1,1 +1,0 @@
1 -view,comment,edit
XWiki.XWikiRights[2]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Groups
... ... @@ -1,1 +1,0 @@
1 -Collabs.tvb-synthetic-resting-state-dataset._.groups.collab-tvb-synthetic-resting-state-dataset-administrator
Levels
... ... @@ -1,1 +1,0 @@
1 -view,comment,edit,delete