Hi Stephanie,

I looked at the data you had uploaded last week. There were a couple difficulties, but they could be gotten around without too much trouble. Mainly, partial coverage had to be taken care of with the -partial_coverage option for the align_epi_anat.py script, and I took your suggestion to handle the large non-uniformity for this data with 3dUniformize. It should be emphasized here that 3dUniformize was definitely *not* made to handle this kind of data, so please, please review the output for this operation carefully. 3dUniformize only expects single sub-brick datasets, so only a single sub-brick is specified as input.

These are the steps I used to align your data:

# slice timing correction
3dTshift -cubic -prefix r1_ts jq_r1+orig

# time series volume registration (registered to first sub-brick)
3dvolreg -base 0 -input r1_ts+orig. -prefix r1_ts_vr

# uniformity correction (use first sub-brick)
3dUniformize -prefix r1_ts_vr_sb0 -anat r1_ts_vr+orig'[0]'

# align anat to epi (use partial_coverage option)
align_epi_anat.py -partial_coverage -anat jq_expvol+orig -epi r1sb0u+orig. \
-suffix _al2epi -epi_base 0 -volreg off -tshift off -anat2epi

# alternatively align epi to anat using uniform sub-brick as base
align_epi_anat.py -partial_coverage -anat jq_expvol+orig -epi r1sb0u+orig. \
-suffix _al2anat -epi_base 0 -volreg off -tshift off -epi2anat \
-child_epi r1_ts_vr+orig.