Can you cofirm you are using the latest version of dcm2niix (1.0.20190410)?
 For a graphical interface, make sure you are using MRIcroGL version 1.2.20190410. If you are using the command line, use version you can get the latest version (1.0.20190410) from Github. 

If you are having problems with the latest version, the first thing I would do is check the providence of your image. dcm2niix uses the proprietary Siemens CSA header to glean a lot of information about your sequence, so make sure this was not removed by a DICOM anonymization stage.

Finally, if you are using a Siemens Vida scanner (software XA10, XA11), you need to be very careful to NEVER save data to mosaic format, as Siemens strips relevant information from Vida mosaics (technically the XA10 mosaics are not valid DICOMs as they lack Type 1 attributes). This is not a limitation of dcm2niix, but rather a limitation of the files Siemens generates.

If none of these thoughts resolve your problem, please post a new issue on the dcm2niix Github page.