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Kinematics of the upper cervical spine during head rotation were investigated using three-dimensional magnetic resonance imaging (MRI) in healthy volunteers.To demonstrate in vivo intervertebral coupled motions of the upper cervical spine.Although various in vivo and in vitro studies have identified the normal movement patterns of the upper cervical spine, no previous studies have accurately analyzed in vivo three-dimensional intervertebral motions of the upper cervical spine during head rotation.Fifteen healthy volunteers underwent three-dimensional MRI of the upper cervical spine using a 1.0-T imager in progressive 15° steps during head rotation. Segmented three-dimensional MRIs of each vertebra in the neutral position were superimposed over images taken at other positions, using voxel-based registration. Relative motions between occiput (Oc) and atlas (C1) and between C1 and axis (C2) were measured and described with 6 degrees of freedom by rigid body Euler angles and translations.Mean (± SD) maximum angles of axial rotation in Oc–C1 and C1–C2 were 1.7 ± 1.5° and 36.2 ± 4.5° to each side, respectively. Increases in angle of axial rotation in C1–C2 became smaller with increased head rotation, indicating axial rotation in C1–C2 displayed nonlinear motion. Coupled lateral bending with axial rotation was observed in the direction opposition to that of axial rotation in Oc–C1 (mean, 4.1 ± 1.4°) and C1–C2 (mean, 3.8 ± 3.0°). Coupled extension with axial rotation occurred at both C0–C1 (mean, 13.3 ± 4.9°) and C1–C2 (mean, 6.9 ± 3.0°).We developed an innovative in vivo three-dimensional motion analysis system using three-dimensional MRI. In vivo coupled motions of the upper cervical spine investigated using this system supported the results of the previous in vitro study.