Computational protocol: Analysis of head impact exposure and brain microstructure response in a season long application of a jugular vein compression collar: a prospective, neuroimaging investigation in American football

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Protocol publication

[…] All MRI data were acquired on the same 3 T Philips Achieva MRI scanner (Philips Medical Systems, Best, the Netherlands) using a 32-channel head coil. The diffusion tensor imaging (DTI) data were acquired with a spin echo-planar imaging sequence with the following specifications: repetition time/echo time (TR/TE)=9000/83 ms; field of view (FOV)=256×256 mm; matrix=128×128; in-plane resolution=2×2 mm; slice thickness=2 mm; 72 slices. Diffusion-weighted images were acquired along 61 non-collinear directions with 7 non-diffusion-weighted images (b0=1000 s/mm2). A high-resolution, three-dimensional (3D) T1-weighted anatomical dataset was acquired in the sagittal direction with the following specifications: TR/TE=8.1/3.7 ms; TI=1070 ms; FOV=256×256 mm; matrix=256×256; in-plane resolution=1×1 mm; slice thickness=1 mm; 180 slices. Susceptibility-weighted imaging (SWI) was also performed (venous blood-oxygen-level dependent (BOLD), TR/TE=14.7/20.7 ms, FOV=220×220 mm, flip angle=10°, matrix=220×221, slice thickness=2 mm). One board-certified neuroradiologist (JLL), blinded to treatment group assignment, evaluated all anatomical images (3D T1-weighted and SWI images). Clinically significant findings were reported to the study investigators, participants and parents as per study protocol. On subjective evaluation of any of the anatomical images (T1-weighted and SWI images), there were no traumatic abnormalities identified. There were no changes between the preseason and postseason anatomical images in any participant, and there was no evidence of any intracranial complication (eg, brain haemorrhage or lesion) from collar use.DTI data were processed with the Functional MRI of the Brain (FMRIB) Software Library (FSL) software package ( In FSL, skull stripping was performed using the brain extraction tool (BET) function. Eddy current and head motion artefact were corrected in FSL by aligning diffusion-weighted images to the first b0 image with an affine transformation with 12 degrees of freedom. The following four commonly used DTI measures were calculated using standard methods: fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD) and radial diffusivity (RD). The tract-based spatial statistics (TBSS) approach was used in the image analysis in the present study. This is a method developed to ameliorate the registration error at the boundary of narrow WM fibre bundles, a common source of error in voxel-based style analysis. Studies have shown that TBSS can effectively reduce the granularity and improve accuracy during normalisation. We followed standard TBSS analysis steps that have been summarised in many previous studies. A skeleton threshold of 0.2 was used in the present study. […]

Pipeline specifications

Software tools FSL, BET
Organisms Homo sapiens
Diseases Hyperemia, Cerebrovascular Trauma