There are two files to convert from DICOM to NifTi, the T1 structural image and the diffusion-weighted image (dwi). Input for each was the raw DICOM file, output is a NifTi file. The -f option indicates the file name for the output--t1 and dwi. The affirmative -x option indicates that the file will be cropped and reoriented; the "n" after the -z option indicates that the structural T1 file will not be compressed, whereas the "y" indicates that the T2 diffusion-weighted (DWI) will be compressed. There are two additional outputs for the DWI data besides the NIfTI files, a .bval file, a file containing b-values (the amount of diffusion weighting for each volume), and a .bvec file, a gradient diffusion table containing the b-vectors (the gradient directions).