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Chunk #3 — Method — MRI acquisition, image processing and statistical analyses

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STRUCTURAL AND FUNCTIONAL CONNECTIVITY IN POSTTRAUMATIC STRESS DISORDER: ASSOCIATIONS WITH FKBP5.
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Scanning was conducted on a research-dedicated Siemens 3-Tesla TIM-Trio scanner at Emory University Hospital. Diffusion-weighted images were acquired with maximum gradient strength of 40mTm−1 with the following parameters: 39×2.5 mm thick axial slices, matrix = 128×128, field of view (FOV) = 220×220 mm, voxel size = 1.72×1.72×2.5 mm. Diffusion weighting was isotropically distributed along 60 directions using a b-value of 1,000 s/mm2. Four normalization images, with no diffusion encoding (b=0), were acquired and averaged for each direction using linear rigid body registration (FLIRT; 30). All diffusion-weighted image processing and analysis was conducted using FMRIB Software Library (FSL version 4.1; www.fmrib.ax.ac.uk/fsl; 31). A high-resolution T1-weighted structural scan was also acquired for co-registration purposes using an MPRAGE sequence: 176 slices, FOV= 256 mm cubic voxels; 1mm isotropic slices; repetition time (TR)= 2600 msec; echo time (TE) = 3.02 msec; inversion time (TI)= 900msec; flip angle=8°. Resting state functional MRI were acquired using the Z-SAGA pulse sequence, which has been shown (32) to recover susceptibility signal losses including amygdala and prefrontal cortex. Volumes were acquired axially, parallel to the anterior-posterior commissure line; 150