Computational protocol: The connectomes of males and females with autism spectrum disorder have significantly different white matter connectivity densities

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Protocol publication

[…] All image processing was undertaken using the LONI Pipeline environment (http://pipeline.loni.usc.edu). First, for each subject, DWI and MRI volumes were affinely co-registered. Eddy current correction was then applied to each DWI volume, which was subsequently processed in TrackVis 6.0 (http://trackvis.org) using its Diffusion Toolkit 0.6 utility to correct for the oblique scan prescription of the Siemens MRI scanner. Tensors were then fit to the DWI data to perform diffusion tensor imaging using default parameters and to then reconstruct fiber streamlines using deterministic tractography. The algorithm used for the latter was fixed step-length streamline propagation. Individual streamlines exhibiting a turning angle below 60 degrees were discarded. The cortical surface of the brain was reconstructed as a triangular tessellation with ~300,000 vertices (average inter-vertex distance: ~1 mm) to produce an anatomically faithful, smooth representation of the GM/WM interface. At each vertex vi of the tessellation, cortical thickness was measured in FreeSurfer 6.0 as the distance between the GM/WM boundary and the brain surface. For each brain hemisphere, a total of 74 cortical structures (gyri and sulci) were identified and parceled in FreeSurfer 6.0 using a probabilistic atlas, as described elsewhere. The brain stem was also segmented in FreeSurfer as well, for a total of 165 parcels over the entire brain. Neuroanatomical labels were assigned to voxels based on probabilistic information estimated from a manually labeled training set. The method uses the previous probability of a tissue class occurring at a specific atlas location and the probability of the local spatial configuration of labels given each tissue class. The technique is comparable in accuracy with manual labeling. Subsequent to parcellation, the surface area, volume and mean curvature of each structure were calculated. The white matter connectivity calculation was performed as described elsewhere. […]

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