Hi Rick,
My command was:
@auto_tlrc -base <path to>/TT_EPI+tlrc -input paraR+orig[1]
-where paraR+orig is my motion-corrected time series
I then put my bucket data into tlrc by using:
adwarp -apar paraR_1_at+tlrc. -dpar para-v-rest+orig. -dxyz 4
-where para-v-rest is my contrast of interest. I wanted to stay with the original resolution for my analyses.
However, the resullt paraR_1_at+tlrc. is shifted down with respect to my T1-weighted scan (that has been put into Talairach space). Is this an alignment issue? I should also note that this is 3T data that was not field-map corrected, so distortions loom large.