Turner & Levine

“Augmented neural activity during executive control processing following diffuse axonal injury”

Supplementary Data: fMRI Methods

fMRI scanning and analyses

Scanning was performed on a 3.0 TMRI system (Signa 3T94 hardware, VH3M3 software; GeneralElectric Healthcare, Waukesha, WI). A volumetric anatomical MRI was performed beforefunctional scanning, using standard high-resolution 3D T1-weighted fast spoiled gradient echo (FSPGR) images (TR/TE=7.2/3.1 ms, inversion-recovery prepared T1=300 ms, flipangle 15°, 256×192 acquisition matrix, 124 axial slices 1.4 mmthick, voxel size=0.86×0.86 cm, FOV=22×16.5 cm). Functional scans wereobtained using a single-shot T2*-weighted pulse with spiral in-out,achieving 26 slices, each 5 mm thick (TR/TE=2000/30 ms, flipangle 70°, 64×64 acquisition matrix, voxel size=3.125×3.125, slice spacing=0, FOV=20×20 cm).Data processing and analyses were performed using Analysisof Functional NeuroImages software1. Timeseriesdata were motion and slice-timing corrected and submitted to a deconvolution analysis using the AFNI plugin3dDeconvolve. The functional data were modeled using a general linear model to derive parameter estimates and corresponding t-statistics for the impulse response functions corresponding to the four conditions (alphabetize 3/5, maintain 3/5) as well as the two types of probe trials (probe 3-letter, probe 5-letter). The resulting whole brain, voxel-based maps of the parameter estimates and their statistical (T-statistic) assessments (i.e. the within subject, within condition activation maps) were transformed into stereotaxic space1, 2. Activation maps were spatially smoothedwith a Gaussian filter with a full width at half maximum value of 8.0 mm to minimize individual variation of the anatomicallandmarks. These steps were performed to facilitate the subsequentgroup analysis, which consisted of voxelwise, mixed effects(groups fixed, conditions fixed, subjects random), three-factorANOVA for unbalanced designs. This program is included as a MATLAB script with the AFNI software package. The three fixed factors each had two levels: Group (TBI, Control subjects), Executive Demand (Alphabetize, Maintain) and Set Size (3 letters, 5 letters). The fourth random factor, subject, was nested within Group. Task effects within groups were thresholded at an individual voxel probability of p<0.0001, with clusters >150 μl (3 acquisition voxels), and having a connectivity radius of 2 mm (i.e., twoclusters need to be separated by at least 2 mm to be considereddifferent). For the interaction of Group x Executive Demand, we report clusters of activation thresholded at p < .001, cluster size > 150 μl. Region of interest analyses were drawn at these cluster maxima to assess the impact of inter-individual variability and potential speed of processing effects. Parameter estimates from each voxel for each condition were extracted from these ROIs and outliers defined as having scores more than 1.5 times the inter-quartile range of their respective groups for each condition were trimmed using a Winsorizing procedure to 2 SD above or below the true mean (i.e. exclusive of the outlier). This procedure allows the maintenance of extreme observations without unduly influencing statistical estimates.

  1. Cox RW, Hyde JS. Software tools for analysis and visualization of fMRI data. NMR Biomed 1997;10:171-178.
  2. Talairach J, Tournoux P. Co-Planar Stereotaxic Atlas of the Human Brain. New York: Thieme Medical Publishers, Inc., 1988.