We have described the methods for image analysis in detail elsewhere +(9, +41, +42), and will briefly summarize them here.
We performed automatic whole brain extraction and interhemispheric brain extraction with removal of nonbrain tissue +(43). Each brain slice was also manually edited such that only brain tissue and CSF remained in each image volume. Reliability of manual scalp editing was determined by calculating the intraclass correlation coefficients for brain volumes from 10 test brains that were randomly mixed in among a larger data set +(42). Intra- and interrater reliability achieved in our laboratory were both >0.99.
Each scan was corrected for signal intensity inhomogeneities. A radiofrequency bias field correction algorithm eliminated intensity drifts attributable to scanner field inhomogeneity, using a histogram spline sharpening method +(44).
Fully automated tissue classification used a partial volume correction method +(45) to automatically classify voxels as most representative of gray matter, white matter, and CSF.
Brain volumes were transformed into standard International Consortium for Brain Mapping-305 space using a 12-parameter linear, automated image registration algorithm +(46).
The cortical surface for each MR volume was extracted by using automated software +(47, +48).
As seen in +Figure 1, we traced 17 sulcal and gyral landmarks on the lateral surface and 12 sulci and gyral landmarks on the interhemispheric surface of each hemisphere employing previously validated anatomic delineation protocols +(41, +42, +49). In addition to contouring the major sulci, a set of six midline landmark curves bordering the longitudinal fissure were outlined on each hemisphere. Interrater variability of manual outlining was measured as the three-dimensional root mean square difference in millimeters between 100 equidistant points from each sulcal landmark traced in six test brains (H.D.) relative to a gold standard arrived at by a consensus of raters as previously reported +(42, +49) (http://www.loni.ucla.edu/~esowell/new_sulcvar.html). Intrarater reliability was computed by comparing the three-dimensional root mean square distance between equidistant surface points from sulcal landmarks from one test brain traced six times by the same rater (H.D.). Three-dimensional root mean square disparities were <2 mm, and on average <1 mm, between points for all landmarks within and between raters.
Cortical pattern matching used the sulcal/gyral landmarks and the cortical surface models from each subject to compute a three-dimensional vector deformation field, which reconfigures each subject’s anatomy into the average pattern of a given group by matching equivalent landmark points in x, y, and z coordinates +(41, +50, +51).
Gray matter proportion measurements used the three-dimensional deformation vector fields obtained from the cortical pattern matching methods to allow a local measurement of gray matter to be made at equivalent three-dimensional cortical surface locations in each subject, referencing corresponding point locations in spatially registered tissue classified scalp-edited brain volumes. Cortical gray matter was quantified by measuring the proportion (or density) of voxels segmenting as gray matter within a sphere with a fixed radius of 15 mm at homologous cortical surface points in each individual. Therefore, at each point on the cortical surface, a local measurement of gray matter is made that may be averaged and compared statistically to provide maps indexing very local differences in tissue proportion within and between groups +(9, +41, +42, +49).