You are looking at the deprecated code for dcm2nii, development ceased on that tool in 2015 (this is why the final versions of dcm2nii urged users to upgrade to dcm2niix). dcm2nii has been superseded by dcm2niix. Vendors are continually updating their use of DICOM, so I would strongly discourage users from using dcm2nii anymore (with the exception of archival work with proprietary formats that predate DICOM). The cropping code for dcm2niix is the function nii_saveCrop(). The code finds the brightest slice in the head-foot direction, which typically corresponds roughly to the center of the brain (ventricular CSF for T2, anterior commissure for T1). It then looks for most superior slice that exceeds 9% of this value. It then crops any slices that are more than 169mm inferior of that slice.