Computational protocol: Regional vulnerability of longitudinal cortical association connectivity

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Protocol publication

[…] Imaging was acquired on a 1.5 T General Electric System (Ge-Medical Systems, Milwaukee, WI) using a pediatric head coil. Diffusion tensor images were acquired using the following parameters: echo-planar imaging (EPI) sequence, TE/TR = 80/10,000 ms, field of view = 22 cm, matrix = 128 × 128, in-plane resolution of 2.5 mm, 25 directions and b-value of 1000 s/mm2.Standard pre-processing steps were performed using routines in FSL. Subject DTI images were motion and eddy current corrected using a rigid body registration, followed by brain extraction using Brain Extraction Tool (BET). DTI metrics, including fractional anisotropy (FA), signal intensity without diffusion weighting (S0), value of the principal eigenvalue (L1), and direction of the principal eigenvector were computed for each voxel. [...] Deterministic tractography was performed using in-house software written in IDL (, Boulder, CO). Streamlines were computed from each voxel with FA > 0.25 in both directions. Stopping thresholds for the tractography were: turning angle >45° or FA < 0.25.The DTI data were segmented into 76 anatomical regions by applying the automated anatomic labeling (AAL) template (). The AAL parcellation atlas was normalized into each subject's native space by applying the reverse of the transformation found for the template based VBM-like analysis. This procedure obtains the greater between-participant accuracy obtainable via a study-specific template, while also ensuring that the template corresponds to MNI space. The anatomical scans were without gross anatomical abnormalities which could conceivably impact the spatial transformations () and all transformations were verified via visual inspection.Each of the 76 regions in the parcellation atlas served as a node in the subsequent topological analyses. 76-×-76 adjacency matrices were constructed for each subject, with each non-diagonal element containing one if there was at least one streamline connecting the two regions, and zero if not. […]

Pipeline specifications

Software tools BET, AAL
Application Magnetic resonance imaging
Organisms Homo sapiens
Diseases Cerebral Palsy, Leukomalacia, Periventricular, Leukoencephalopathies