Dunedin Brain Imaging Study MRI Protocol
Diffusion Tensor Imaging
MRI Data Acquision and Processing
Each participant was scanned using a MAGNETOM Skyra (Siemens Healthcare GmbH) 3T scanner equipped with a 64-channel head/neck coil (due to size constraints, 7 participants were scanned with a 20-channel head/neck coil) at the Pacific Radiology Group imaging center in Dunedin, New Zealand. Diffusion-weighted images providing full brain coverage were acquired with 2.5 mm isotropic resolution and 64 diffusion weighted directions (4700 ms repetition time, 110.0 ms echo time, b value 3,000 s/mm2, 240 mm field of view, 96×96 acquisition matrix, slice thickness=2.5 mm). Non-weighted (b=0) images were acquired in both the encoding (AP) and reverse encoding (PA) directions to allow for EPI distortion correction.
Diffusion images were processed in FSL (http://fsl.fmrib.ox.ac.uk/fsl). Raw diffusion-weighted images were corrected for susceptibility artifacts, subject movement, and eddy currents using topup and eddy. Images were then skull-stripped and fitted with diffusion tensor models at each voxel using FMRIB's Diffusion Toolbox (FDT; http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT). The resulting FA images from all subjects were non-linearly registered to the FA template developed by the Enhancing Neuro Imaging Genetics Through Meta-Analysis consortium (ENIGMA), a minimal deformation target calculated across a large number of individuals (Jahanshad et al., 2013). The images were then processed using the tract-based spatial statistics (TBSS) analytic method (Smith et al., 2006) modified to project individual FA values onto the ENIGMA-DTI skeleton. Following the extraction of the skeletonized white matter and projection of individual FA values, average FA across the full skeleton and average FA within tract-wise regions of interest from the intersection of the skeleton and the 27 regions in the Johns Hopkins University (JHU) white matter parcellation atlas (Mori et al., 2005) were calculated. After visual inspection of all diffusion images, 7 study members were removed because data was collected with 20 channel head coils leading to poor diffusion image quality, 3 were removed due to major incidental findings, 5 were removed due to excessive (>3mm) motion detected with the eddy tool, and 6 were removed due to missing diffusion scans. This resulted in 854 study members with quality diffusion images that were included in the analysis. Test-retest reliability, as assessed in 20 Dunedin Study members (mean interval between scans = 79 days), was excellent (ICC=.956 for whole brain average FA, and mean ICC=.879 across 27 tracts)
References
Jahanshad N, Kochunov PV, Sprooten E, Mandl RC, Nichols TE, Almasy L, Blangero J, Brouwer RM, Curran JE, de Zubicaray GI, Duggirala R, Fox PT, Hong LE, Landman BA, Martin NG, McMahon KL, Medland SE, Mitchell BD, Olvera RL, Peterson CP, Starr JM, Sussmann JE, Toga AW, Wardlaw JM, Wright MJ, Hulshoff Pol HE, Bastin ME, McIntosh AM, Deary IJ, Thompson PM, Glahn DC. 2013. Multi-site genetic analysis of diffusion images and voxelwise heritability analysis: a pilot project of the ENIGMA-DTI working group. Neuroimage 81():455-69.
Mori S, Wakana S, Van Zijl PC, Nagae-Poetscher LM. 2005. MRI atlas of human white matter. Amsterdam: Elsevier.
Smith SM, Jenkinson M, Johansen-Berg H, Rueckert D, Nichols TE, Mackay CE, Watkins KE, Ciccarelli O, Cader MZ, Matthews PM, Behrens TE. 2006. Tract-based spatial statistics: voxelwise analysis of multi-subject diffusion data. Neuroimage 31(4):1487-505.