Hi there,

I'm currently using dcm2niix, version:  Chris Rorden's dcm2niiX version 25Nov2016 (64-bit Linux)

I have noticed a small things that I thought I would report:

If I'm using the BIDS flag -b y, then the -o flag to save output to another directory doesn't seem to work.  NIFTI and JSON are always saved to the input folder.

Workaround is:  if I set isBIDS=1 in the .dcm2nii.ini, then I can use dcm2niix with -o to get the output folder.

Thanks!
Jenny

Sorry I did not see this message earlier, but seems to be fixed with the current versions, e.g. 
 ./dcm2niix -b y -f %p_%s -o ~/tst ~/tst_t1
saves the results to the "tst" rather than "tst_t1" folder