Through the ANTs cortical thickness pipeline, brain tissue was segmented into 6 specific regions of interest (ROIs).  Intensity values of the ROI image ranged from 1 through 6, and corresponded in ascending order, respectively, to cerebrospinal fluid, gray matter, white matter, the basal ganglia, the brain stem, and the cerebellum.  Six tissue priors were created, of corresponding to each of the six ROIs converted into probability masks.  Accomplishing this tissue segmentation through ANTs was essential in order to highlight the cortex and strip away structures that were not of interest.   Various other files were generated, including a single value brain mask ROI image and a similar brain mask overlay.   
    After running the ANTs cortical thickness program on the template image, all participants were analyzed individually through the pipeline.  To run participants serially without creating individual job scripts for each participant, a for loop was created in a new batch script in vi text editor.  This for loop cycled through participants, and submitted a job for each of them.