The alignment files were subjected to local realignment and de-duplication using the Genome Analysis Toolkit (GATK) [ 36] and Picard [ 37].
For each participant, functional images were subjected to spatial realignment to the mean image, slice time correction to the middle slice, reorientation, normalization to a standard EPI template based on the Montreal Neurological Institute (MNI) reference brain, and smoothing with an isotropic 8 mm full-width half-maximum Gaussian kernel.
The BAM files were reformatted using the Picard-tools reheader command, then subjected to local realignment around indel sites using the genome analysis toolkit GATK [ 54] to remedy alignment issues associated with small indel polymorphisms occurring near the beginnings and/or ends of the short reads.
Motion parameters calculated during the realignment stage of preprocessing were subjected to statistical analysis to establish whether volunteers moved more during sedation.
After recalibration and local realignment using the Genome Analysis Toolkit (GATK version 1.0.5974) [ 15], the refined sequencing results were subjected to variant calling using a toolkit (Atlas2) [ 16].
The authors recommend appropriate follow-up of these subjects to assess need for realignment surgery.
We then carried out within-subject realignment to account for head motion.
EPI volumes were realigned to the first volume for each subject to correct for interscan movement, and unwarped for static magnetic field inhomogeneities using field maps [37] and for movement-induced inhomogeneities using realignment parameters [38].
The demands on the legitimation of law change with this functional realignment: to be legitimate, modern law must secure the private autonomy of those subject to it.
Due to realignments, the current alignment of Route 23 bypasses the intersection of these two turnpikes.
To correct for motion artifacts, subject-specific realignment parameters were included in the general linear model.
