Similar protocols

Pipeline publication

[…] ped with a 12-channel head coil located at the UCSF Neuroscience Imaging Center. Whole brain images were acquired using volumetric magnetization prepared rapid gradient-echo sequence (MPRAGE; TR/TE/TI = 2300/2.98/900 ms, α = 9°). The field of view was 240×256 mm, with 1×1 mm in-plane resolution and 1 mm slice thickness. Diffusion imaging data were acquired via a spin-echo, echo planar imaging sequence with 55 slices 2 mm thick (TR/TE = 8000/109 ms, FOV = 220 mm, matrix = 100×100) in two series. One series contained diffusion gradients and 64 diffusion directions (b = 0 and b = 2000 s/mm2, 1 average) while the other had no diffusion gradients and 6 diffusion directions (b = 0, 10 averages)., FreeSurfer: The T1 MPRAGE structural MR images were analyzed using the FreeSurfer image analysis suite, which is documented and freely available for download online at: http://surfer.nmr.mgh.harvard.edu. FreeSurfer is a surface-based structural MRI analysis tool that segments white matter and tessellates both gray and white matter surfaces . Previous publications have provided detailed descriptions and validation of the software , . After initial automated segmentation through FreeSurfer version 5.1, each subject’s image was individually checked for quality and accuracy of segmentation. Inaccuracies in grey and white matter segmentation, as well as inaccurate pial boundaries and residual skull fragments were manually corrected with FreeSurfer’s built-in editing software. These cases were then reprocessed to take edits into account and final volumes were recalculated. Intracranial volume (ICV) was calculated based on FreeSurfer’s own eTIV (estimated total intracranial volume) metric, which uses atlas normalization as well as the relationship between the linear transform to MNI305 space and ICV., Tract-Based Spatial Statistics: DTI data were eddy current corrected using FMRIB’s Diffusion Toolbox (FSL 4.1.6; http://fsl.fmrib.ox.ac.uk/fsl) . Brain extraction and binary brain mask creation took place using the b0 image through the FSL Brain Extraction Tool. Fractional Anisotropy (FA) maps were created based on the diffusion tensor modeling results from FSL DTIFIT. Whole brain white matter analysis was conducted using FSL’s TBSS protocol . All subjects’ FA data were registered using the nonlinear registration tool FNIRT to the IXI Aging DTI Template masked by a study-specific binary averaged image. The mean FA and mean FA skeleton were created from the study sample. Each subject’s aligned FA data was then projected onto the mean FA skeleton and the resulting data fed into voxelwise cross-subject statistics., Cognitive testing was obtained within 3 months of the participants’ blood draw and neuroimaging scan. Considering the strong association between both aging and slower processing speed , as well as lower fractional anisotropy and slower processing speed , , participants were administered a series of processing speed tasks, and were asked to make rapid judgments about stimuli presented on the lapt […]

Pipeline specifications

Software tools FreeSurfer, BET, FSL