A.) To see the options for dcm2nii, run the command "dcm2nii" from the command line. It will not only report the options but also the location of the preferences file. For MacOS and Linux this will be the ".dcm2nii" folder in your home directory. Since the folder name starts with a "." it is hidden by default. There are many options, but here are three simple ones:
 1.) From your finder, choose Go/GoToFolder... and enter "~/.dcm2nii"
 2.) From your terminal, type "nano ~/.dcm2nii/dcm2nii.ini"
 3.) From your terminal, type "open -a textedit ~/.dcm2nii/dcm2nii.ini"

B.) You may also want to consider dcm2niix (which comes with MRIcroGL). While I hope that dcm2nii (which comes with MRIcron) is mature and useful, it is not under active development and I only update it when users report issues. You can use MRIcroGL's "Import" menu item to run dcm2niix from the graphical interface, or you can run it from the terminal.


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$ ./dcm2nii
Chris Rorden's dcm2nii :: 30APR2016 64bit BSD License
reading preferences file /Users/rorden/.dcm2nii/dcm2nii.ini
Either drag and drop or specify command line options:
dcm2nii
OPTIONS:
-4 Create 4D volumes, else DTI/fMRI saved as many 3D volumes: Y,N = Y
...
-x Reorient and crop 3D NIfTI images: Y,N = N
You can also set defaults by editing /Users/rorden/.dcm2nii/dcm2nii.ini
EXAMPLE: dcm2nii -a y /Users/Joe/Documents/dcm/IM_0116