1. Neuroscience
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Temporal transitions of spontaneous brain activity

  1. Zhiwei Ma
  2. Nanyin Zhang  Is a corresponding author
  1. The Pennsylvania State University, United States
Research Article
Cite this article as: eLife 2018;7:e33562 doi: 10.7554/eLife.33562
10 figures, 1 data set and 1 additional file

Figures

Schematic illustration of the data analysis pipeline.
https://doi.org/10.7554/eLife.33562.002
Figure 2 with 5 supplements
An example of a RSFC spatial pattern.

Left: seed region; Mid: RSFC pattern of the seed. Color bar indicates t values; Right: average of rsfMRI frames matched to the RSFC pattern. Color bar shows BOLD amplitude. Distance to bregma is listed at the bottom of each slice. CC: spatial correlation coefficient between the average of rsfMRI frames (Right) and the corresponding seed map (Mid).

https://doi.org/10.7554/eLife.33562.003
Figure 2—figure supplement 1
Characteristic RSFC patterns (1-8) in the awake rat brain.

Left: seed region; Mid: RSFC pattern of the seed; Right: average of rsfMRI frames matched to the RSFC pattern. Distance to bregma for each slice is the same as those shown in Figure 2. CC: spatial correlation coefficient between the average of rsfMRI frames and the corresponding seed map.

https://doi.org/10.7554/eLife.33562.004
Figure 2—figure supplement 2
Characteristic RSFC patterns (9-16) in the awake rat brain.

Left: seed region; Mid: RSFC pattern of the seed; Right: average of rsfMRI frames matched to the RSFC pattern. Distance to bregma for each slice is the same as those shown in Figure 2. CC: spatial correlation coefficient between the average of rsfMRI frames and the corresponding seed map.

https://doi.org/10.7554/eLife.33562.005
Figure 2—figure supplement 3
Characteristic RSFC patterns (17-24) in the awake rat brain.

Left: seed region; Mid: RSFC pattern of the seed; Right: average of rsfMRI frames matched to the RSFC pattern. Distance to bregma for each slice is the same as those shown in Figure 2. CC: spatial correlation coefficient between the average of rsfMRI frames and the corresponding seed map.

https://doi.org/10.7554/eLife.33562.006
Figure 2—figure supplement 4
Characteristic RSFC patterns (25-32) in the awake rat brain.

Left: seed region; Mid: RSFC pattern of the seed; Right: average of rsfMRI frames matched to the RSFC pattern. Distance to bregma for each slice is the same as those shown in Figure 2. CC: spatial correlation coefficient between the average of rsfMRI frames and the corresponding seed map.

https://doi.org/10.7554/eLife.33562.007
Figure 2—figure supplement 5
Characteristic RSFC patterns (33, 35-40) in the awake rat brain.

Left: seed region; Mid: RSFC pattern of the seed; Right: average of rsfMRI frames matched to the RSFC pattern. Distance to bregma for each slice is the same as those shown in Figure 2. CC: spatial correlation coefficient between the average of rsfMRI frames and the corresponding seed map.

https://doi.org/10.7554/eLife.33562.008
Figure 3 with 3 supplements
Reproducibility of the RSFC pattern transitions.

(a) RSFC pattern transition matrices of subgroups 1 and 2 without regression of spatial similarities between reference RSFC patterns. (b) RSFC pattern transition matrices of subgroups 1 and 2 with regression of spatial similarities between reference RSFC patterns. Entries in each transition matrix were normalized to the range of [0, 1].

https://doi.org/10.7554/eLife.33562.009
Figure 3—figure supplement 1
Reproducibility of RSFC pattern transitions between two subgroups of rats with relatively high (FD above median, right panels) and low (FD below median, left panels) motion levels without (top panels) and with (bottom panels) regression of RSFC pattern similarities.
https://doi.org/10.7554/eLife.33562.010
Figure 3—figure supplement 2
Distribution of the reproducibility of RSFC pattern transition matrices between randomly divided subgroups across 10000 trials.

Left: without regression of RSFC pattern similarities. Right: with regression of RSFC pattern similarities. Red lines: the reproducibility of RSFC pattern transition matrices between FD-based group division with (right) and without (left) regression of RSFC pattern similarities.

https://doi.org/10.7554/eLife.33562.011
Figure 3—figure supplement 3
RSFC pattern transitions at different motion censoring threshold.

Left: RSFC pattern transition matrices at the motion censoring threshold of FD <0.1 mm without (top) and with (bottom) regression of RSFC pattern similarities. Right: RSFC pattern transition matrices at the motion censoring threshold of FD <0.2 mm without (top) and with (bottom) regression of RSFC pattern similarities. The correlations between the RSFC pattern transition matrices at FD <0.1 mm and those at FD <0.2 mm were 0.83 and 0.88 with and without regression of seed map similarities, respectively.

https://doi.org/10.7554/eLife.33562.012
Thresholded group-level RSFC pattern transition matrix after regression of RSFC pattern similarities.

Rows/columns are arranged based on the brain system of the seed regions. Numbers next to/below rows/columns correspond to the seed map number in Figure 2 and Figure 2—figure supplement 1.

https://doi.org/10.7554/eLife.33562.013
Community structures of the RSFC pattern transition network.

The thresholded transition matrix in Figure 4 was used as the adjacency matrix to generate a directed weighted graph. The layout of nodes was based on a force-field algorithm (Jacomy et al., 2014). The node number corresponds to the seed map number in Figure 2 and Figure 2—figure supplement 1—5. Inlet: seed regions of RSFC patterns colored coded based on the community affiliations of nodes (i.e. RSFC patterns).

https://doi.org/10.7554/eLife.33562.014
Top: Seed regions of RSFC patterns with hub score ≥1, color coded based on the hub score.

No color was given to seed regions of RSFC patterns with hub score = 0. Bottom: the brain systems of seed regions.

https://doi.org/10.7554/eLife.33562.015
Transition patterns of hub networks.

Green arrows denote bidirectional transitions between RSFC patterns. Orange arrows denote unidirectional transitions between RSFC patterns. Pattern numbers correspond to the seed map numbers shown in Figure 2 and Figure 2—figure supplement 1—5. The brain system of the seed for each pattern is listed in the circle. Th and Hypoth, Thalamus and Hypothalamus; HP and RetroHP, Hippocampus and Retrohippocampus.

https://doi.org/10.7554/eLife.33562.016
Reproducibility of temporal transitions between 333 characteristic RSFC patterns in humans.

The transition matrices of two randomly divided subgroups (a) without regression of RSFC pattern similarities (b) with the regression of RSFC pattern similarities.

https://doi.org/10.7554/eLife.33562.017
Thresholded group-level RSFC pattern transition matrix in humans (permutation test, p<0.05, FDR corrected).

Rows/columns are grouped based on the brain system of the seed.

https://doi.org/10.7554/eLife.33562.018
Hub scores of RSFC patterns in humans displayed on their seed regions.

The boundary of nodes was color coded based on the brain system (right). Nodes with hub score ≥3 were defined as hubs (yellow-filled nodes).

https://doi.org/10.7554/eLife.33562.019

Data availability

The following previously published data sets were used
  1. 1
    The Human Connectome Project S1200 Data Release
    1. Van Essen DC
    2. Smith SM
    3. Barch DM
    4. Behrens TE
    5. Yacoub E
    6. Ugurbil K
    (2013)
    Open access dataset available from ConnectomeDB (https://db.humanconnectome.org/app/template/Login.vm). Account registration is required and access to certain data elements such as family structure is subject to restricted use terms (please see http://www.humanconnectome.org/study/hcp-young-adult/data-use-terms).

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