I attempted to convert a folder of DICOMs into a 3D NifTI object.  However when I try to run it with dicoms who's pixel data has been compressed, it it gives me the same error for each slice:

"FFFE,E000,Image Fragment[0@112126]=0 Offset112126 Length0"

Can dcm2nii deal with compressed pixel data and I'm missing that option, or is that not supported? Thank you.

I would be happy to look at your image and make sure my software provides users with clear instructions on how to proceed. dcm2niiX can handle the following formats
  https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Transfer_Syntaxes_and_Compressed_Images
while dcm2nii includes all these except JPEG2000. Please also see the web page for my caveats with regards to story compressed DICOM data. Due to these concerns I would personally suggest storing DICOM images in one of the uncompressed formats. Indeed because DICOM headers are so large, you may find that general compression methods outperform the DICOM-specific compression