Computational protocol: Awareness of Emotional Stimuli Determines the Behavioral Consequences of Amygdala Activation and Amygdala-Prefrontal Connectivity

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[…] Image distortions from eddy currents and head motion were compensated using an affine transformation within the FSL (FMRIB Software Library) package (http://fsl.fmrib.ox.ac.uk/fsl). Distortions resulting from magnetic field inhomogeneities were corrected for with the B0 field map and PRELUDE (phase region expanding labeler for unwrapping discrete estimates) and FUGUE (FMRIB’s utility for geometrically unwarping EPIs) within FSL. FSL’s BET (Brain Extraction Tool) was used to isolate the brain tissue. Tensor fitting was performed using CAMINO (http://cmic.cs.ucl.ac.uk/camino/).A population-specific standard space template was created using all participants’ DTI images with the Diffusion Tensor Imaging Tookit (DTI-TK) (http://www.nitrc.org/projects/dtitk). The unbiased template is constructed so that both the average diffusion features (e.g. FA) and anatomical features (tract size) in the population are accounted for. The individual tensor maps were normalized to the template with rigid, affine, and diffeomorphic alignments and interpolated to 2 × 2 × 2 mm3 voxels. DTI-TK was used to calculate FA maps in normalized space.Individual tensor volumes in standard space underwent tractography to reconstruct white matter pathways. The tractography was performed on the whole brain using the TEND algorithm in CAMINO. In order to achieve a seed file for tractography, a white matter mask was defined as FA > 0.15 and the stopping criteria was FA < 0.15. Uncinate fasciculus extraction was performed using a standard protocol, which entails the placement of temporal and frontal waypoint ROIs in each hemisphere using TrackVis (AND conjunction), and averaging FA values for each right and left set of uncinate fasciculus fibers. The frontal and temporal waypoint ROIs used for the uncinate fasciculus extraction are shown in . We report the results of the original L and R FA variables (which were fully replicated when age and whole-brain FA were controlled for). […]

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