Computational protocol: Human brain networks function in connectome-specific harmonic waves

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Protocol publication

[…] From T1-weighted MRI data of each subject (resolution 0.7 mm), we reconstruct the cortical surfaces separating the white and grey matter, referred to as the white matter surface in the rest of the manuscript, as well as grey matter and the cerebrospinal fluid, referred to as the grey matter surface in the rest of the manuscript, separately for each hemisphere using the Freesurfer Software We register each cortical surface to the 1,000 subject average cortical surface of the cortical parcellation data (in the rest of the manuscript referred to as average subject, represented by 20,484 vertices), in order to allow for the vertex-to-vertex comparison between the connectome harmonics and the 1,000 subject averaged reference of the resting state networks.From the DTI data of each subject (resolution 1.25 mm), we extract the white matter cortico-cortical and thalamo-cortical fibres by applying a deterministic tractography algorithm using the MATLAB implementation of Vista Lab, Stanford University After registering the DTI data and the cortical surface of each subject, we initialize the seeds for tractography on the cortical surface separating the white and grey matter. Centred around each vertex (node)—in total 20,484—we initialize eight seeds and perform the tractography with the following parameters: fractional anisotropy threshold 0.3, that is, fractional anisotropy <0.3 being termination criteria for the tracking, minimum tract length 20 mm, and maximum angle between two contiguous tracking steps 30°. […]

Pipeline specifications

Software tools FreeSurfer, VISTASOFT
Application Magnetic resonance imaging
Organisms Homo sapiens