Many DICOM systems save each 2D slice as a single file. Others, (e.g. Siemens Mosaic format) save each 3D image from a 4D time series as a separate file. On the other hand, NIfTI expects all 2D slices to be stacked as a single 3D file (and optionally all 3D volumes in a fMRI/DTI dataset as a single 4D dataset). Therefore, it is common to have fewer NIfTI images than DICOM images.
  
You can find some of my tutorials here
  http://www.mccauslandcenter.sc.edu/crnl/psyc589888

I would strongly encourage you to heed the warning you see whenever you run dcm2nii: consider upgrading to dcm2niix. You can get dcm2niix as a standalone tool
  https://github.com/rordenlab/dcm2niix/releases
or with MRIcroGL (providing the graphical control from the "Import" menu:
  https://github.com/neurolabusc/MRIcroGL

A verbose manual is here 
  https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage