Fixing a bug found for niftis without proper freqdim and phasedim fields.
Adding initialization code for freq,phase and slice dims as well as more comments to niftiApplyXform for the bug.
Removed the initialization code for fields that should be properly set in the underlying NIFTI structure.
Merge pull request #28 from vistalab/bugFixFreqDim

Added error checking for easy fail over if required nifti fields are not correctly set.