The options and features of dcm2niix are described here
https://www.nitrc.org/plugins/mwiki/inde...
The new software does not create reoriented or cropped images. Now that NIfTI has become popular I think most tools will be able to read the spatial orientation matrix from the header. Also, there are more sophisticated methods for cropping images, here is what I use
https://github.com/neurolabusc/spmScript...