Hi Daniel,

Thank you for the prompt answer.
I have tried the script you suggested. I concatenated 2 epi runs for analysis.

align_epi_anat.py -anat spgr_T1+orig -epi all_runs.ppm002+orig -epi_base 0 -tlrc_apar spgr_T1_at+tlrc -epi2anat -suffix _al2anat -volreg off -child_epi stats.ppm002+orig

A couple of new datasets have been generated. For example, stats.ppm002_tlrc_al2anat+tlrc* and stats.ppm002_al2anat+orig* are what I am interested in.

However, the coef subbricks are still missing in those datasets and the stats datasets do not align with anatomical run well in either talairach or original view. The attached is the sample picture of the alignment.

Any suggestion?

Thanks a lot,
Iris