Dear Chris,

I have a set DWI data in PAR/REC format. I used dcm2niix to convert my data to nifti format with accompanying bvec and bval files. After attempting to create FA maps from my nifti files, most of my data resulted in empty FA maps, showing basically the brain mask I used and no FA data.

I went through all the files to figure out where the problem is, and then I realised that the nifti files which produced empty FA maps had abnormally low bvec values in their bvec files. All the nifti files which produced proper FA maps had bvec values somewhere between 0.09 and 0.9, while the ones which failed to produce FA maps had values around 0.001-0.05. 

Interestingly enough, when I used one of the "normal" bvec files to produce FA maps from the problematic nifti files, I got normal looking FA maps. So I'm almost certain the problem is with the bvec files.

This is really strange, as all the data was collected using the same scanner (Philips) and protocol.

Do you think there might be a problem with the conversion process (from PAR/REC to nfiti)? I know my question is a bit convoluted and maybe not directly related to dcm2nii, but I thought you might have some insight to share. Thanks for your time.

Best,
Shereif