Computational protocol: Quantifying uncertainty in brain network measures using Bayesian connectomics

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Protocol publication

[…] All preprocessing was performed using FSL 5.0 ( Structural scans were segmented using FAST (Zhang et al., ) and FIRST (Patenaude et al., ). The preprocessing steps for the diffusion data were conducted using FSL FDT (Behrens et al., ) and consisted of correction for eddy currents and estimation of the diffusion parameters. We used FDT Probtrackx 2.0 (Behrens et al., , ) for probabilistic streamlining, where gray matter voxels served as targets while voxels on the gray-white matter boundary served as seeds. The target mask was a combination of the gray matter mask output from FAST and the interior voxels of the subcortical segmentation from FIRST, this mask also served as termination mask. The seed mask consisted of the mixeltype mask representing the mixture of gray and white matter voxels from FAST combined with the boundary mask for the subcortical structures from FIRST. Overlap between seed and target mask was removed from the seed mask.For each of the seed voxels 5000 streamlines were drawn, with a maximum length of 2000 steps (step size was 0.5 mm). Streamlines were stopped when they reached a voxel in the target mask. Streamlines were restricted by fractional anisotropy and they were discarded if a sharp angle (<80°) occurred or their length was less than 2 mm. The output thus obtained is a matrix N, where nij is the number of streamlines drawn from voxel i in the seed mask to voxel j in the target mask. This matrix was collapsed into 90 cortical and subcortical areas as defined by the AAL atlas (excluding cerebellum). Streamlines were summed over all voxels per region, resulting in a 90 × 90 aggregated connectivity matrix which ranges over regions rather than voxels. The aggregated streamline count matrices are freely available through […]

Pipeline specifications

Software tools Probtrackx, AAL
Applications Magnetic resonance imaging, Diffusion magnetic resonance imaging analysis
Organisms Homo sapiens