afni.nimh.nih.gov

Hi Janani,
The EPI you sent me is not a timeseries EPI, it is likely the output of 3dDeconvolve.
What you need for alignment is the EPI time series. If you used 3dDeconvolve's output in 3dAllineate, you will certainly not get a decent alignment.
In any case, I would still like to have the EPI timeseries to test the new alignment procedure.
cheers,
ziad