Hi Rick and Daniel,
Thanks. I've been away from this for a bit. I added -volreg_base to prevent "-child_epi" errors, but I am still getting some errors. I forgot to include the "-tshift off" option, but it sounds like that is probably not the problem. I will add it to the next run.
From the various errors, it seems like the program want to, but can't, overwrite directories/files. I have again attached the program and the feedback with the list of errors. Any suggestions would be great.

Thanks.
Darren

@auto_tlrc -base ~/abin/TT_N27+tlrc -input s"$id"anat_shft+orig
align_epi_anat.py -big_move \
-anat s"$id"anat_shft+orig -epi s"$id"hum1R_tshift_card_shft+orig \
-epi_base median -volreg_base 5 -suffix al2anat \
-child_epi s"$id"hum"?"R_tshift_card_shft+orig.HEAD \
-AddEdge -epi2anat \
-tlrc_apar s"$id"anat_shft_at+tlrc


++ ###########################################################
#Script is running:
rm -f AddEdge/*
#++ Applying transformation for epi to anat for @AddEdge
#Script is running (command trimmed):
3dAllineate -base s07anat_shft+orig -1Dmatrix_apply 's07hum1R_tshift_card_shftal2anat_mat.aff12.1D' -prefix __tt_s07hum1R_tshift_card_shft_alnd_rs -input __tt_s07hum1R_tshift_card_shft_vr_ts_rs_ns+orig -master BASE
++ 3dAllineate: AFNI version=AFNI_2008_07_18_1710 (Dec 12 2008) [64-bit]
++ Authored by: Emperor Zhark
++ Loading datasets
++ ========== Applying transformation to 1 sub-bricks ==========
++ ========== sub-brick #0 ==========
++ Output dataset ./__tt_s07hum1R_tshift_card_shft_alnd_rs+orig.BRIK
++ total CPU time = 0.0 sec
++ ###########################################################
#Script is running:
mkdir AddEdge
mkdir: cannot create directory `AddEdge': File exists
#Script is running (command trimmed):
3dcopy -overwrite __tt_s07anat_shft_ns+orig AddEdge/s07anat_shft_ns
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (Dec 12 2008) [64-bit]
#Script is running (command trimmed):
3dcopy -overwrite __tt_s07hum1R_tshift_card_shft_vr_ts_rs_ns+orig AddEdge/s07hum1R_tshift_card_shft_ns
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (Dec 12 2008) [64-bit]
#Script is running (command trimmed):
3dcopy -overwrite __tt_s07hum1R_tshift_card_shft_alnd_rs+orig AddEdge/s07hum1R_tshift_card_shftal2anat
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (Dec 12 2008) [64-bit]
#Script is running (command trimmed):
cd AddEdge; @AddEdge s07anat_shft_ns+orig s07hum1R_tshift_card_shft_ns+orig s07hum1R_tshift_card_shftal2anat+orig; cd ..
** ERROR: output dataset name 's07hum1R_tshift_card_shftal2anat' conflicts with existing file
** ERROR: dataset NOT written to disk!
failure: cannot write dataset, exiting...
++ 3dMean: AFNI version=AFNI_2008_07_18_1710 (Dec 12 2008) [64-bit]
++ 3dAutobox: AFNI version=AFNI_2008_07_18_1710 (Dec 12 2008) [64-bit]
+++ Executing 3dcalc()
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (Dec 12 2008) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type short brick(s)
++ Sub-brick 0 scale factor = 9.230141
++ Computing output statistics
++ Output dataset /tmp/3dcalc#0001+orig.BRIK
++ Auto bbox: x=48..217 y=22..160 z=19..163
++ output dataset: ./tmp_box+orig.BRIK
++ 3dedge3: AFNI version=AFNI_2008_07_18_1710 (Dec 12 2008) [64-bit]
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (Dec 12 2008) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./_ae.s07anat_shft_ns_e+orig.BRIK
++ 3dedge3: AFNI version=AFNI_2008_07_18_1710 (Dec 12 2008) [64-bit]
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (Dec 12 2008) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./s07hum1R_tshift_card_shft_ns_e+orig.BRIK
3dBrickstat: Command not found.

perc: Subscript out of range.
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (Dec 12 2008) [64-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset _ae.epi_sc+orig
invalid input dataset <_ae.s07anat_shft_ns_s07hum1R_tshift_card_shft_ns_e+orig>
++ 3dedge3: AFNI version=AFNI_2008_07_18_1710 (Dec 12 2008) [64-bit]
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (Dec 12 2008) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./s07hum1R_tshift_card_shftal2anat_e+orig.BRIK
3dBrickstat: Command not found.

perc: Subscript out of range.
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (Dec 12 2008) [64-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset _ae.epi_sc+orig
invalid input dataset <_ae.s07anat_shft_ns_s07hum1R_tshift_card_shftal2anat_e+orig>
Recommended commands:
(make sure you kill all pre-existing AFNI sessions first)
afni -niml -yesplugouts &
@AddEdge
#++ Creating final output: epi data aligned to anat
# copy is not necessary
#++ Saving history
#Script is running:
3dNotes -h "align_epi_anat.py -big_move -anat s07anat_shft+orig -epi \
s07hum1R_tshift_card_shft+orig -epi_base median -volreg_base 5 -suffix \
al2anat -child_epi s07hum?R_tshift_card_shft+orig.HEAD -AddEdge -epi2anat \
-tlrc_apar s07anat_shft_at+tlrc" s07hum1R_tshift_card_shftal2anat+orig

*+ WARNING: Over-writing dataset ./s07hum1R_tshift_card_shftal2anat+orig.HEAD
#++ Parent /home/newfmri/HSC2007Projects/s07/session/humour/s07hum1R_tshift_card_shft+orig: Child: /home/newfmri/HSC2007Projects/s07/session/humour/s07hum?R_tshift_card_shft+orig
#Script is running (command trimmed):
3dAttribute TAXIS_OFFSETS s07hum?R_tshift_card_shft+orig
#++ Can not do time shifting of slices. Data is already time shifted
Error: Second index j=1 is >= to number of elements (1) in 0th line of output
Traceback (most recent call last):
File "/home/newfmri/abin/align_epi_anat.py", line 2497, in ?
ps.process_child_epi(child_epi)
File "/home/newfmri/abin/align_epi_anat.py", line 2340, in process_child_epi
child.epi_ts, child.epi_vr, child.epi_ns = \
File "/home/newfmri/abin/align_epi_anat.py", line 2086, in process_epi
if(ps.dry_run() or \
File "/home/newfmri/abin/afni_base.py", line 409, in dset_dims
dl = [int(com.val(0,0)), int(com.val(0,1)), int(com.val(0,2)), int(com.val(0,3))]
TypeError: int() argument must be a string or a number