Hi Rick,
Thanks for your interest. The codes that are relavent are:

3dDeconvolve -polort 2 -input all_runs+orig -num_stimts 12 \
-stim_file 1 "../../hrf2_pre2.1D" -stim_label 1 pre2 \
-stim_file 2 "../../hrf2_pre5.1D" -stim_label 2 pre5 \
-stim_file 3 "../../hrf2_pre3.1D" -stim_label 3 pre3 \
-stim_file 4 "../../hrf2_post2.1D" -stim_label 4 post2 \
-stim_file 5 "../../hrf2_post5.1D" -stim_label 5 post5 \
-stim_file 6 "../../hrf2_post3.1D" -stim_label 6 post3 \
-stim_file 7 "dfile.all.1D[0]" -stim_base 7 \
-stim_file 8 "dfile.all.1D[1]" -stim_base 8 \
-stim_file 9 "dfile.all.1D[2]" -stim_base 9 \
-stim_file 10 "dfile.all.1D[3]" -stim_base 10 \
-stim_file 11 "dfile.all.1D[4]" -stim_base 11 \
-stim_file 12 "dfile.all.1D[5]" -stim_base 12 \
-num_glt 10 \
-gltsym "SYM: pre2 pre3 pre5 -post2 -post3 -post5" -glt_label 1 preVSpost \
-gltsym "SYM: pre2 -pre3" -glt_label 2 pre2VSpre3 \
-gltsym "SYM: pre2 -pre5" -glt_label 3 pre3VSpre5 \
-gltsym "SYM: pre3 -pre5" -glt_label 4 pre3VSpre5 \
-gltsym "SYM: post2 -post3" -glt_label 5 post2VSpost3 \
-gltsym "SYM: post2 -post5" -glt_label 6 post2VSpost5 \
-gltsym "SYM: post3 -post5" -glt_label 7 post3VSpost5 \
-gltsym "SYM: pre2 -post2" -glt_label 8 pre2VSpost2 \
-gltsym "SYM: pre3 -post3" -glt_label 9 pre3VSpost3 \
-gltsym "SYM: pre5 -post5" -glt_label 10 pre5VSpost5 \
-fout -tout -bucket subj_func -fitts subj_fitts -xjpeg subj_xmat.jpg -x1D subj_xmat.x1D

3dbucket -prefix {$subj_name}_betas+orig subj_func+orig'[1,4,7,10,13,16]'
adwarp -apar {$subj_name}+tlrc -dxyz 3 -dpar {$subj_name}_betas+orig

all_runs+orig is the big dataset, which is the concataneted scaled (in percentile signal change) datasets
hrf2_pre2.1D is the ideal waveform for finger2 for pre scan (i.e. prior to treatment)
pre3 is for finger 3 for pre scan
pre5 is for finger 5 for pre scan
post2 is for finger2 for post scan (i.e. after treatment)
dfile.all includes 6 registreration parameters (e.g. roll, pitch, etc.)
subj_func+orig'[1,4,7,10,13,16]' includes pre2#0_Coef, pre5#0_Coef, etc.

My question is:
After running 3dANOVA, difference maps for finger 2 (pre2 vs post2)demonstrated stastistically significant negative z statistics in some regions . I need to demonstrate fmri signal decrease in these regions as a result of treatment. A reviewer recommends me to show group maps of pre and post scans for finger 2 in SEPARATE figures and a table with % signal change. However, I could not figure out how I can make a group analysis and obtain a group map separetly for pre2 and post2. I am confused, because I am trying to obtain a group map for ONE condition (e.g. pre2) with no comparison between conditions (e.g pre2 vs post2). Should I run a test like independent-samples to t-test to examine whether signal changes for one condition (e.g. pre2) is different from 0 for obtaining such a figure ?

A similar figure that I am trying to obtain is the Figure 2 in Napadow et al. 2007, [www.nmr.mgh.harvard.edu]

Thanks in advance,
Ozcelik