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.