Hi I have four sets of functional data that are obtained before and after two sets of anatomical data. I used @auto_tlrc for transformation. I used align_epi_anat to align these EPI data to respective anatomical and tlrc transformation.

I have preprocessed data then to use 3dDeconvolve for final analysis. (please see attached script).

# Arash Babaei
# Medical College of Wisconsin
# Date: 2009.10.1

cd af1/SW3post
set ANA = 'anat2'
set EPI = 'SW3post'

# Remove cardiovascular noise from resting state data
rm -f ${EPI}_icor+orig*
3dretroicor -ignore 4 -prefix ${EPI}_icor -resp ${EPI}_resp.1D -card ${EPI}_puls.1D ${EPI}+orig

# Perform Talairach transformation of anatomical image
rm -f ${ANA}_at+tlrc*
rm -f ${ANA}_ns+orig*
rm -f ${ANA}_al_mat.aff12.1D*
rm -f ${ANA}_ns.Xaff12.1D*
rm -f ${ANA}_ns_WarpDrive.log*
@auto_tlrc -base TT_icbm452+tlrc -input ${ANA}+orig

# Volume register & align functional data to anatomical data
rm -f ${EPI}_icor_al+orig*
rm -f ${EPI}_icor_tlrc_al+tlrc*
rm -f ${EPI}_icor_al_mat.aff12.1D*
rm -f ${EPI}_icor_al_reg_mat.aff12.1D*
rm -f ${EPI}_icor_al_tlrc_mat.aff12.1D*
rm -f ${EPI}_icor_tsh_vr_motion.1D*
align_epi_anat.py -anat ${ANA}+orig -epi ${EPI}_icor+orig \
-epi2anat \
-epi_base 5 \
-epi_strip 3dAutomask \
-tlrc_apar ${ANA}_at+tlrc

# Remove spikes from resting state data
rm -f ${EPI}_dspk+orig*
3dDespike -ignore 4 -cut 2.5 4.0 -prefix ${EPI}_dspk ${EPI}_icor_al+orig

# Remove trend from resting state data
rm -f ${EPI}_dspk+orig*
3dDetrend -prefix ${EPI}_dtrn -polort 2 ${EPI}_dspk+orig

# Perform spatial smoothing
rm -f ${EPI}_blur+orig*
3dmerge \
-doall \
-1blur_fwhm 4.0 \
-prefix ${EPI}_blur \
${EPI}_dspk+orig

# Make high resolution wm anat mask
rm -f ${ANA}_wm+orig*
3dcalc \
-a ${ANA}_ns+orig \
-expr "step(a-3200)" \
-prefix ${ANA}_wm

# Make high resolution csf anat mask
rm -f ${ANA}_csf+orig*
3dcalc \
-a ${ANA}_ns+orig \
-expr "step(a)*step(1050-a)" \
-prefix ${ANA}_csf

# Create mask for in-brain voxels
rm -f ${EPI}_msk+orig*
3dAutomask -dilate 1 -prefix ${EPI}_msk ${EPI}_blur+orig'[5]'

# Transform high resolution wm anat mask to low resolution wm EPI mask
rm -f ${EPI}_wm+orig*
3dfractionize -template ${EPI}_msk+orig \
-input ${ANA}_wm+orig \
-clip 0.90 -prefix ${EPI}_wm

# Transform high resolution csf anat mask to low res csf EPI mask
rm -f ${EPI}_csf+orig*
3dfractionize -template ${EPI}_msk+orig \
-input ${ANA}_csf+orig \
-clip 0.6 -prefix ${EPI}_csf

# Extract time series average over wm voxels
3dmaskave -quiet -mask ${EPI}_wm+orig \
${EPI}_blur+orig > ${EPI}_wm.1D

# Extract time series average over csf voxels
3dmaskave -quiet -mask ${EPI}_csf+orig \
${EPI}_blur+orig > ${EPI}_csf.1D

# Orthogonlize functional data to motion parameters, csf, and wm
rm -f ${EPI}_fit*
rm -f ${EPI}_irf*
rm -f ${EPI}_err*
rm -f ${EPI}_res*
rm -f seed.xmat.1D*
rm -f seed.REML_cmd
3dDeconvolve \
-input ${EPI}_blur+orig \
-mask ${EPI}_msk+orig \
-jobs 2 \
-CENSORTR 435..510 \
-polort A \
-nfirst 3 \
-num_stimts 9 \
-basis_normall 1 \
-stim_times 1 '1D:150 510' 'TENT(5,100,15)' \
-stim_label 1 seed \
-stim_file 2 "${EPI}_icor_tsh_vr_motion.1D[0]" -stim_base 2 -stim_label 2 Roll \
-stim_file 3 "${EPI}_icor_tsh_vr_motion.1D[1]" -stim_base 3 -stim_label 3 Pitch \
-stim_file 4 "${EPI}_icor_tsh_vr_motion.1D[2]" -stim_base 4 -stim_label 4 Yaw \
-stim_file 5 "${EPI}_icor_tsh_vr_motion.1D[3]" -stim_base 5 -stim_label 5 dS \
-stim_file 6 "${EPI}_icor_tsh_vr_motion.1D[4]" -stim_base 6 -stim_label 6 dL \
-stim_file 7 "${EPI}_icor_tsh_vr_motion.1D[5]" -stim_base 7 -stim_label 7 dP \
-stim_file 8 "${EPI}_wm.1D" -stim_base 8 -stim_label 8 wm \
-stim_file 9 "${EPI}_csf.1D" -stim_base 9 -stim_label 9 csf \
-gltsym 'SYM: +seed' \
-glt_label 1 seed \
-float \
-iresp 1 ${EPI}_irf \
-bout \
-fout \
-rout \
-tout \
-fitts ${EPI}_fit \
-errts ${EPI}_err \
-bucket ${EPI}_res



echo "Preprocessing ************** Finished"


#End of script
#3dAllineate -cubic -1Dmatrix_apply SW3post_al_tlrc_mat.aff12.1D -prefix SW3post_volresults+tlrc SW3post_volresults+orig

1- I used to be able to joggle between orig and tlrc when I manually transformed to tlrc my data. It appears that name tag with auto-tlrc and align_epi_anat is different so it does not do that automatically. Is there a reason for that?could I just change the names to EPI+tlrc or anatomical to anat+tlrc ? I want to be able to look at where am I? option on my functional data where I have significant difference.

2-If I want to look at my results in +tlrc, could I transform my results with EPI_al_tlrc_mat.aff12.1D using 3dallineate to results +tlrc or I should run 3dDeconvolve on my EPI+tlrc data again to obtain desirable results?

3- In each individual if I need to align all of the scans together (anat2 to anat1) and all functionals to them (EPI1& EPI2&EPI3 & EPI4) what is the best way for alignment to have least interpolation