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Chunk #10 — Materials and methods — Genotyping, CNV detection and structural measurements

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Association of genetic copy number variations at 11 q14.2 with brain regional volume differences in an alcohol use disorder population.
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Structural MRI data were collected on a 3-Tesla Siemens Trio scanner. High resolution T1-weighted anatomic images were acquired with a 5-echo multi-echo MPRAGE sequence with TE = 1.64 ms, TR = 2.53 s, TI = 1.2 s, flip angle = 7°, number of excitations = 1, slice thickness = 1 mm, field of view = 256 mm, resolution = 256 × 256. Cortical reconstruction and volumetric segmentation was performed with the Freesurfer image analysis suite, which is documented and freely available for download online at (http://surfer.nmr.mgh.harvard.edu/). The technical details of these procedures are described in (Dale, Fischl, & Sereno, 1999; Fischl, Sereno, & Dale, 1999; Han et al., 2006). This processing includes motion correction and averaging (when available) of multiple T1 weighted images (Reuter, Rosas, & Fischl, 2010), removal of non brain tissue using a surface deformation method (Ségonne et al., 2004), Talairach transformation, segmentation of sub cortical white matter and deep gray matter structures (hippocampus, amygdala, caudate, putamen, ventricles), intensity normalization, tessellation of the gray matter white matter boundary, automated topology correction and surface deformation following intensity gradients. Following