Construction of individual structural brain networks
This protocol is extracted from research article:
Cognitive chimera states in human brain networks
Sci Adv, Apr 3, 2019; DOI: 10.1126/sciadv.aau8535

Whole-brain structural connectivity matrices were constructed for each individual (subject) using a bootstrapping approach. To minimize the impact of bias in the tractography parameter scheme on streamline generation, whole-brain fiber tractography (52) was performed 100 times for each participant, generating 250,000 streamlines per iteration. Across the 100 iterations, values were randomly sampled for quantitative anisotropy based fiber termination thresholds (0.01 to 0.10), turning angle thresholds (40 to 80), and smoothing (50 to 80%), while constant values were used for step size (1 mm) and minimum/maximum fiber length thresholds (10 mm/400 mm). On each iteration, a binary connectivity matrix was generated, where an edge between two regions of interest was considered present if 5% or more of streamlines generated were found to connect them. The probability of observing a connection was estimated by calculating the frequency of detecting an edge across all 100 iterations. The regions of interest were determined using cortical components of the Desikan-Killiany atlas and subcortical components of the Harvard-Oxford subcortical atlas. In the resulting weighted matrices, connection strengths were normalized by the sum of the regional brain volumes, and these normalized matrices were used as the structural representations of individual brains. All analyses were performed using DSI Studio ( and MATLAB (MathWorks Inc., Natick, MA, USA).

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