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Chunk #15 — Materials and Methods — Imaging Preprocessing and Registration

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The effect of alcohol priming on neural markers of alcohol cue-reactivity.
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yes

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FSL 4.1 (FMRIB’s Software Library, www.fmrib.ox.ac.uk/fsl) was used for the imaging analyses. Motion correction was carried out using the Motion Correction Linear Image Registration Tool (McFLIRT, Version 5.0) with the estimated motion parameters entered as covariates in the general linear model. Non-brain tissue/skull removal was conducted with the Brain Extraction Tool (BET). The images were high-pass filtered (100s cutoff) in the temporal domain with the FMRI Expert Analysis Tool (FEAT, Version 5.63), using a Gaussian-weighted straight line fit. The EPI images were first registered to the MBW, then to the MPRAGE using affine linear transformations, and finally into standard (Montreal Neurological Institute, MNI avg152 template) space for between subject analyses, refined by FSL’s FNIRT nonlinear registration (24). Contrast images were smoothed using a FWHM Gaussian kernel (5mm). Three subjects (two G-allele carriers and one A-allele homozygote) were excluded from further analyses due to excessive motion (exceeding 3mm of translation).