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Chunk #14 — Methods — MRI data acquisition, processing and statistical analysis

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Effects of alcohol use initiation on brain structure in typically developing adolescents.
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MRI data were collected on a Siemens 3 T scanner (Siemens Medical Systems, Erlangen, Germany) using an eight-channel array head coil at the University of Minnesota. Three-dimensional T1 weighted brain images were acquired in the coronal plane using a magnetization prepared rapid gradient echo (MPRAGE) sequence (TR = 2530 ms, TE = 3.65 ms, TI = 1100 ms, flip angle = 7°, 240 slices, no gap, voxel size = 1.0 × 1.0 × 1.0 mm, FOV = 256 mm). Diffusion weighted brain images were acquired by applying gradients in 12 noncollinear directions in the axial plane using a dual spin echo, single-shot, pulsed-gradient, echo-planar imaging (EPI) sequence (TR = 12.5 s, TE = 99 ms, 64 slices, no gap, voxel size = 2.0 × 2.0 × 2.0 mm, FOV = 256 mm, 2 averages, b value = 1000 s/mm2). For off-line EPI geometric distortion correction, b0 field maps were constructed from two gradient-echo images acquired using different echo times (TE = 4.62 ms and 7.08 ms; TR = 700 ms, flip angle = 90°, 64 slices, no gap, voxel size = 2.0 × 2.0 × 2.0 mm, FOV = 256 mm).