Active contour segmentation and its robust implementation using level set methods are well established theoretical approaches that have been studied thoroughly in the image analysis literature. Despite the existence of these powerful segmentation methods, the needs of clinical research continue to be fulfilled, to a large extent, using slice-by-slice manual tracing. To bridge the gap between methodological advances and clinical routine, we developed an open source application called ITK-SNAP, which is intended to make level set segmentation easily accessible to a wide range of users, including those with little or no mathematical expertise. This paper describes the methods and software engineering philosophy behind this new tool and provides the results of validation experiments performed in the context of an ongoing child autism neuroimaging study. The validation establishes SNAP intra/interrater reliability and overlap error statistics for the caudate nucleus and finds that SNAP is a highly reliable and efficient alternative to manual tracing.Analogous results for lateral ventricle segmentation are provided.

Generalized enlargement of gray and white matter cerebral volumes, but not cerebellar volumes, are present at 2 years of age in autism. Indirect evidence suggests that this increased rate of brain growth in autism may have its onset postnatally in the latter part of the first year of life.

Objective Brain enlargement has been observed in 2 year old children with autism but the underlying mechanisms are unknown. This longitudinal MRI study investigated early growth trajectories in brain volume and cortical thickness. Method Cerebral gray and white matter volumes and cortical thickness in children with autism spectrum disorder and controls were examined. Subjects were seen at approximately 2 years of age (autism = 59, controls = 38) and were rescanned approximately 24 months later at age 4–5 years (autism = 38, controls = 21). Results We observed generalized cerebral cortical enlargement in individuals with ASD at both 2 and 4 – 5 years of age. Rate of cerebral cortical growth across multiple brain regions and tissue compartments, in individuals with ASD, was parallel to that seen in controls, indicating that there was no increase in rate of cerebral cortical growth during this interval. No cerebellar differences were observed in ASD. After controlling for TBV, a disproportionate enlargement in temporal lobe white matter was observed in the ASD group. We found no differences in cortical thickness, but an increase in an estimate of surface area in the ASD group compared to controls for all cortical regions measured (temporal, frontal, and parietal-occipital). Conclusions Our longitudinal MRI study found generalized cerebral cortical enlargement in children with ASD, with a disproportionate enlargement in temporal lobe white matter. There was no difference from controls in the rate of brain growth for this age interval, indicating brain enlargement in ASD results from an increased rate of brain growth prior to age 2. The presence of increased cortical volume, but not cortical thickness, suggests that early brain enlargement may be associated with increased cortical surface area. Cortical surface area overgrowth in ASD may underlie brain enlargement and implicates a distinct set of pathogenic mechanisms.

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