Dear AFNI and SUMA experts:

Here is my program which I believe creates the original mesh. After concatenation of runs, removal of TPs and doing tshifting, I do the following set of commands below: I wonder if you see anything obviously wrong??? Since I use +orig space anatomical volume and SurfVol, I am guessing the surface meshes are in original space--Is that correct? I wonder how they can be transformed to a standard mesh. I found these commands (see below) from the MapIcosehedron handout and it said you can use these commandlines to transform an original mesh to a given standard mesh. I am wondering if this is the typical way of doing things or if there are any alternatives? Can you use the result called std.141.SUMAfinal.niml.dset found from below in group data analysis such as 3dANOVA2? Obviously, I need all my subjects to be standard before doing group analysis. Anyway, I would appreciate any comments about this because if I don't understand the definitions or am not sure of them in this case, I am in big trouble doing the calculations correctly. I wish all of you great Holidays!

3dWarp -deoblique -prefix scat_runtob cat_runt+orig

3dvolreg -dfile motionsuma -base 'scat_runtob+orig[575]' -prefix scat_runtob_reg scat_runtob+orig

align_epi_anat.py -anat Volumeob+orig -epi scat_runtob_reg+orig -epi_base 575 -epi_strip 3dAutomask -volreg off

@SUMA_AlignToExperiment -exp_anat Volumeob_al+orig -surf_anat SUMASubject06_SurfVol+orig -strip_skull surf_anat -atlas_followers -overwrite_resp S -prefix SUMASubject06_SurfVol_Alnd_Exp

3dVol2Surf -spec SUMASubject06_rh.spec -sv SUMASubject06_SurfVol_Alnd_Exp+orig -surf_A smoothwm -surf_B pial -f_index nodes -f_steps 10 -map_func ave -oob_value 0 -grid_parent scat_runtob_reg+orig -out_niml SUMASubj06VtoS.niml.dset

SurfSmooth -spec SUMASubject06_rh.spec -surf_A smoothwm -input SUMASubj06VtoS.niml.dset -met HEAT_07 -target_fwhm 6.0 -output SUMASubj06VtoSblurred.niml.dset

1d_tool.py -infile motionsuma -demean -write motionsuma.demean

3dDeconvolve -input SUMASubj06VtoSblurred.niml.dset -polort 2 -num_stimts 12 \
-stim_file 1 s_PULSE.1D -stim_label 1 "PULSE" -stim_maxlag 1 6 \
-stim_file 2 s_PPI.1D -stim_label 2 "PPI" -stim_maxlag 2 6 \
-stim_file 3 s_PPI2.1D -stim_label 3 "PPI2" -stim_maxlag 3 6 \
-stim_file 4 'motionsuma[1]' -stim_label 4 "Roll" \
-stim_base 4 \
-stim_file 5 'motionsuma[2]' -stim_label 5 "Pitch" \
-stim_base 5 \
-stim_file 6 'motionsuma[3]' -stim_label 6 "Yaw" \
-stim_base 6 \
-stim_file 7 'motionsuma[4]' -stim_label 7 "IS" \
-stim_base 7 \
-stim_file 8 'motionsuma[5]' -stim_label 8 "RL" \
-stim_base 8 \
-stim_file 9 'motionsuma[6]' -stim_label 9 "AP" \
-stim_base 9 \
-stim_file 10 'e_PulseSubject06.1D' -stim_label 10 "e_Pulse" \
-stim_file 11 'e_PPISubject06.1D' -stim_label 11 "e_PPI" \
-stim_file 12 'e_PPI2Subject06.1D' -stim_label 12 "e_PPI2" \
-concat concat.1D \
-bucket DeconmotionSUMA \
-fout -tout -vout -rout -bout

# below lines find the chosen freesurfer parcellation in the lookup table and apply its mask
# to the final .dset to localize any activity to that brain region.
3dcalc -a 'rh.aparc.a2009s.annot.niml.dset[0]' -expr 'equals(a,9211105)' -prefix myinsularoi
3dcalc -a myinsularoi.niml.dset -expr "step(a)" -prefix myinsulanewroi
3dcalc -a myinsulanewroi.niml.dset -b DeconmotionSUMA.niml.dset -expr "a*b" -prefix SUMAfinal.niml.dset

# These are the applied lines from MapIcosahedron that I believe create the standard mesh for a 141 density using the above #SUMAfinal.niml.dset which was found from taking the deconvolution result (i.e. DeconmotionSUMA) after applying the
#freesurfer parcellation above.

SurfToSurf -i_fs std.141.rh.smoothwm.asc \
-i_fs rh.smoothwm.asc \
-prefix std.141. \
-mapfile std.141.SUMASubject06_rh.niml.M2M \
-dset SUMAfinal.niml.dset