Chris,

Thanks for the quick reply. I made the adjustments via command line as you suggested but I am now receiving the buffer overflow using the "-i y" to ignore derived images, which before I was only getting when not ignoring derived images.

Originally:

dcm2niix /path/to/DICOMs -> did not work, buffer overflow
dcm2niix -i y /path/to/DICOMs -> works but missing derived images such as FA associated with DTI
dcm2niigui -> produces all derived images

New following your steps:
./dcm2niix -i y /path/to/DICOMS -> buffer overflow error

_matt