I just wanted to let you know that I've modified the way FreeSurfer stores NIFTI1 files (these are the single .nii and .nii.gz files). The change is somewhat esoteric: the vox_offset is now 352 instead of 348. 352 is the NIFTI spec, so we were technically out of compliance before, though AFNI, FSL, and SPM did not seem to have a problem with it.
doug
freesurfer@nmr.mgh.harvard.edu