White matter pathways were automatically identified using an open-source, freely available software package, Automated Fiber Quantification (AFQ) version 1.2 (
https://github.com/yeatmanlab/AFQ). AFQ
\cite{Yeatman_2012} identifies the core of 20 major fiber tracts and also segments the corpus callosum into eight subsections. The 20 major pathways are the corticospinal tract, inferior longitudinal fasciculus, inferior fronto-occipital fasciculus, uncinate fasciculus, anterior thalamic radiation, cingulum cingulate gyrus and hippocampal bundles, superior longitudinal fasciculus, arcuate fasciculus, and forceps major and forceps minor of the corpus callosum. The eight subsections of the corpus callosum are roughly associated with the orbitofrontal, the anterior frontal, superior frontal, motor, superior parietal, posterior parietal, occipital, and the temporal regions.
The command AFQ_RUN is the main routine to analyze group data. This function runs the full automated pipeline. There are two inputs into AFQ_run: 1) a mat file with the cell array of paths to each subject's DTI data and 2) a mat file containing binary vector of 0s and 1s to identify subjects as patients (1) or controls (0). The command AFQ_Create generates an AFQ structure containing the options for running AFQ. The output are plots of the normal range of the diffusion measurement along each of 20 major fiber tracts. Each subject that is outside this normal range on a given tract was flagged and plotted with respect to the controls.