It sounds like your scans will be composed of several different series, each with different resolutions and FOVs. dcm2niix converts each DICOM series as a separate NIfTI file. Therefore, you will have one NIfTI image per series. You will then want to use a different tool to concatenate them all together as a single file. The NIfTI format requires that all voxels are equidistant, so some interpolation will need to be required if you have different FOVs or distance between slice centers. The task of stitching different series together is outside the remit of dcm2niix, so you will have to use a different tool.