Computational protocol: Cortical activation changes and improved motor function in stroke patients after focal spasticity therapy– an interventional study applying repeated fMRI

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Protocol publication

[…] Pre-processing and analysis were performed using the fMRI Expert Analysis Tool (FEAT) Version 5.91, which is part of the Analysis Group at the Oxford Centre for Functional MRI of the Brain (FMRIB) Software Library (FSL) (see also www.fmrib.ox.ac.uk/fsl). The following pre-statistics were applied: 1) Motion correction using FMRIB’s Linear Image Registration Tool (MCFLIRT) [], 2) non-brain removal using the Brain Extraction Tool (BET) [], 3) spatial smoothing using a Gaussian-shaped kernel with a full width at half maximum (FWHM) of 5 mm, specifying neighborhood size and weighting, 4) grand mean intensity normalization of the entire 4D dataset by a single multiplicative factor, causing all single-session data sets to have the same overall mean intensity, and 5) high-pass temporal filtering (Gaussian-weighted least-squares straight line fitting with sigma = 40.0s) to remove slow unwanted signals (i.e. heart beat, breathing, scanner-related drifts) in each voxel’s time series.The statistical analysis of fMRI time series was carried out using the FMRIB’s Improved Linear Modeling (FILM) with local auto-correction correlation to fit the GLM voxelwise [].In the post-statistics processing of activation images, Z (Gaussianized T/F) statistic images were threshold-using clusters determined by Z > 2.3 and a (corrected) cluster significance threshold of p = 0.05 [].Registration to high resolution structural and/or standard space images was carried out using FLIRT, providing optimization for robust affine (12DOF in 3D) linear registration and motion correction of brain images [].Atlas based analysis of data was performed using the Jülich probability atlas for the left and right primary and secondary motor cortex-specific Brodmann areas 4a, 4p and 6 to cover primary and secondary motor representations, and Eickhoff’s Anatomy Toolbox v1.5, linearly transformed into MNI152 space [-]. For regional probabilistic atlas based analysis parameters were converted to % BOLD signal change. For each probabilistic region of interest (ROI) the activated brain volume (number of adjacent activated voxels) and magnitude of BOLD activity were recorded. […]

Pipeline specifications

Software tools FSL, BET
Applications Magnetic resonance imaging, Functional magnetic resonance imaging
Organisms Homo sapiens
Diseases Stroke
Chemicals Oxygen