Hi Jenna,
The 6s TR seems too long (unless this is for an auditory study).
And while we don't really recommend band passing, if you are going to do it, the TR should be correct.
We ran into a case (I think in ADNI, but am not positive) where the AFNI extension in the NIFTI header was made with a mistake, while the NIFTI header itself was okay. Maybe that applies here.
For one of the DSET.nii EPI datasets, what is the output of these 2 commands?
nifti_tool -disp_hdr -field pixdim -infiles DSET.nii
3dinfo -tr DSET.nii
If they disagree and the NIFTI header says 3s, then yes, go with that.
What do those commands show?
- rick