Similar protocols

Pipeline publication

[…] ariables had the same sign.Table 1Table 1:, High resolution T1-weighted brain images were acquired using a 3D MPRAGE (Magnetization Prepared Rapid Gradient Echo Imaging) protocol with 192 contiguous axial slices, collected in ascending fashion parallel to the anterior and posterior commissures, echo time (TE)=2.32 ms, repetition time (TR)=1900 ms, field of view (FOV)=230 mm, acquisition matrix 256 mm×256 mm, slice thickness=0.90 mm, and flip angle=9°. All images were collected on a Siemens Magnetom Trio 3T whole-body MRI scanner., Automated brain tissue segmentation and reconstruction of the T1-weighted structural MRI images were performed using the standard recon-all processing pipeline in FreeSurfer, version 5.2.0 (Released May, 2013; http://surfer-nmr.mgh.harvard.edu/). This produced estimates of 1) cortical thickness, 2) cortical volumes, 3) sub-cortical volumes, 4) ventricles, and 5) corpus callosum , , , , , . Segmentations and tractography were manually checked for errors. Estimates in the left and right hemispheres were summed to produce bilateral estimates, and all values were converted to z-scores to control for differences in scale. A complete list of estimated structures appears in . FreeSurfer produced automated segmentation that closely approximates hand tracing, but like all segmentation procedures may introduce systematic bias., The diffusion tensor imaging estimates for fractional anisotropy (FA) and radial diffusivity (RD) data was analyzed using tract-based spatial statistics in FSL , , . This pipeline involves fitting a tensor model to the raw diffusion data using fMRIDB׳s diffusion toolbox, and non-brain tissues were removed using FSL׳s brain extraction tool. All subjects׳ FA data were then aligned into a common space using the nonlinear registration tool FNIRT , . Next, the mean FA image was created and thinned to create a mean FA skeleton that represents the centers of all tracts common to the group. Each subject׳s aligned FA data was then projected onto this skeleton to create an estimate of the subject-level value associated with each tract., , , Research reported in this publication was supported by the Intelligence Advanced Research Projects Activity (IARPA), Contract no. 2014-13121700004 to the University of Illinois at Urbana-Champaign. The content is solely the responsibility of the authors and does not necessarily represent the views of IARPA., University of Illinois at Urbana-Champaign, Institutional Review Board study ap […]

Pipeline specifications

Software tools FreeSurfer, BET, FSL