Hello,
 I assume you are running the modern dcm2niix rather than the older dcm2nii. The DICOM standard has evolved a lot since dcm2niix replaced dcm2nii. I would reserve dcm2nii for archival analyses, in particular for proprietary formats that preceded the DICOM standard. I would heed the warning generated wheneve you run dcm2nii that you should consider moving to dcm2niix.

dcm2niix is provided with MRIcroGL
  https://www.nitrc.org/frs/?group_id=889
or you can get it as a standalone program
  https://github.com/rordenlab/dcm2niix/releases

If you do have problems, it would be helpful to know what version you are using - the is the first line displayed regarless of whether you use the graphical Import menu item from MRIcroGL or run the program from the command line:
 Chris Rorden's dcm2niiX version  v1.0.20180622 GCC6.1.0 (64-bit MacOS)
If your version is not the latest stable release (v1.0.20180622) please consider upgrading. You can also build a more recent developmental release (v1.0.20181009) by downloading and compiling the github code. If these do not work with your dataset, consider posting an issue on Github.