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Chunk #7 — METHOD — PREPROCESSING OF FUNCTIONAL IMAGING DATA

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Deficits in functional connectivity of hippocampal and frontal lobe circuits after traumatic axonal injury.
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The images were first converted from DICOM to Analysis of functional NeuroImages (AFNI) readable format. AFNI Software was used for selected preprocessing steps. Slice-time correction was performed to adjust for varying acquisition time for slices. Time series data were corrected for motion and linear drift artifacts. The amount of movement observed on a frame-by-frame basis did not exceed 1 voxel in size for any participant in this study. Given coherence in blood oxygenation level-dependent signal fluctuations occurs at low frequencies, 19, 27, 28 high frequency components were removed prior to analysis of functional connectivity by setting a low-pass filter at 0.12Hz. The signal to noise ratio was then increased by spatially smoothing the data with a 3-dimensional Gaussian tapering function (5 mm full width at half maximum). Functional images were coregistered to high-resolution T1 images for each participant, and masks of regions containing cerebral spinal fluid was created using FSL 4.1.4.29 These masks were used to obtain averaged time series data from regions unlikely to contribute variance of neuronal origin. The time series from these regions were later regressed out from functional data of interest.