4. Cortical Thickness

Cortical thickness, volume and gray matter density were estimated in the DKT atlas using ANTsLongCT v 0.0.9. All output can be found on PMACS in /project/ExtraLong/data/corticalThickness/antslongct5/. Details of the processing steps can be found in the ANTsLongCT wiki. Briefly, the composite warp from the group template space to the session space and its inverse are created. Then, the priors from the group template space are warped to the single subject template (SST) space, where Atropos is performed. The posteriors from Atropos on the SST are used as priors for Atropos on the individual sessions. The segmentation and posteriors resulting from Atropos on the session are then used as input to the Kelly Kapowski cortical thickness estimation algorithm. Finally, regional values are quantified in the DKT atlas, the labels for which are obtained through warping the labels in the group template space to the session space via the composite warped, and taking the intersection between the label set and the cortical thickness image. Gray matter density values are the posterior probabilities of being gray matter, according to the Atropos run on the session images.