2.3 MRI Acquisition and Processing

Scanning was completed at the Neuroimaging Research for Veterans (NeRVe) center at the VA Boston Healthcare hospital on a 3T Siemens MAGNETOM Trio system. During the first part of the scanner session two anatomical magnetization prepared rapid gradient-echo (MP-RAGE) structural scans were obtained with a 12-channel head coil. These MP-RAGE T-1 scans were acquired with the following parameters: repetition time (TR) = 2530ms, echo time (TE) = 3.32ms, flip angle = 7°, acquisition matrix = 256 × 256 × 176, voxel size = 1mm³. Anatomical scans were inspected at acquisition for motion artifacts and repeated if necessary. Following acquisition these scans were averaged to increase signal-to-noise ratio. All structural images were then processed using standard FreeSurfer and Analysis of Functional Imaging (AFNI) pipelines (Cox, 1996; Fischl, Sereno, & Dale, 1999; Fischl et al., 2004).

The functional run was collected using a 32-channel head coil and one whole-brain echo-planar T2*-weighted sequence. The scanning parameters for the functional scan were as follows: TR = 2000ms, TE = 30ms, flip angle = 90°, 248 volumes, acquisition matrix = 64 × 64, in-plane resolution = 3.0 × 3.0 mm², slice thickness = 3.75mm. Following acquisition, the functional scan was processed using AFNI and custom written routines in Matlab (Mathworks Inc., Natick, MA). Preprocessing steps included slice-time correction, motion correction using a 6-parameter, rigid body, least-squares alignment procedure, spatial smoothing with a 6-mm FWHM Gaussian kernel, automated co-registration and normalization of anatomical and functional volumes to Talairach space, and scaling of functional dataset values to percent signal change using the equation x′ = 100* (x − x₀)/x₀, where x₀ was the mean value of the run. During preprocessing, automated segmentation algorithms generated three masks from the Talairached anatomical volume. These included masks covering grey matter, white matter, and cerebral spinal fluid (CSF). Average time series from the functional scan were extracted from eroded white matter and cerebral spinal fluid masks to use as nuisance regressors.