Computational protocol: Hypercapnic evaluation of vascular reactivity in healthy aging and acute stroke via functional MRI

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Protocol publication

[…] All preprocessing of imaging data was performed within the Analysis of Functional Neuroimages (AFNI) suite (), except where noted. Subject-specific gray matter masks were created via automated segmentation of the skull-stripped anatomical volumes using FSL's FAST (FMRIB Software Library, Oxford, UK) (). Functional data were first aligned to the anatomical and normalized to standard Montreal Neurological Institute (MNI) space. The first four volumes were discarded to allow for steady-state imaging. Images were then resampled to 3.0 mm isotropic, despiked, volume-registered, and spatially smoothed using a 4-mm full-width at half-maximum Gaussian kernel. The time series within each voxel was scaled to percent signal and estimated in a general linear model with a canonical gamma variate hemodynamic response function (HRF) convolved with a boxcar reference waveform and six rigid-body motion parameters and their derivatives regressed. A composite estimate of head motion was calculated for each subject as the square root of the sum of squares (Euclidean norm) of the twelve motion parameters' (three translational and three rotational) derivatives (). High-motion time points (Euclidean norm exceeding 0.3) were censored in the GLM. […]

Pipeline specifications

Software tools AFNI, FSL
Application Functional magnetic resonance imaging
Organisms Homo sapiens
Diseases Stroke