Hi, I was wondering if I was correct in assuming that it is better to run signal normalization prior to 3dDeconvolve when there are multiple runs of EPI data.
Also, if this is correct, would the normalization be run on the blurred EPI data or would blurring occur after signal normalization, just prior to 3dDeconvolve? In other words, should I blur each run separately, normalize the signals, then concatenate the runs?
Also, instead of having to write down the clip level that gets put into 3dcalc, is there an easier way to do this, so one doesn't have to stop the script to input the values?

Thanks so much!

Here is my signal normalization script, which I would use prior to concatenation.

#Signal Normalization
#Do a voxel by voxel mean calcuation of the mean intensity value with AFNI '3dTstat'

3dTstat -prefix ${subj}-WOF-1-reg-CR-mean+orig '${subj}-WOF-1-reg-CR+orig[10..$]'
3dTstat -prefix ${subj}-WOF-2-reg-CR-mean+orig '${subj}-WOF-2-reg-CR+orig[10..$]'

#Calculate the Clip level for each run

3dClipLevel ${subj}-WOF-1-reg-CR+orig
3dClipLevel ${subj}-WOF-2-reg-CR+orig

#write down clip levels for each run

#calculate % signal change with AFNI '3dcalc'

3dcalc -a '${subj}-WOF-1-reg-CR+orig' \
-b ${subj}-WOF-1-reg-CR-mean+orig \
-expr "(a/b*100)*step(b-clip level of ${subj}-WOF-1-reg-CR+orig)"
-prefix ${subj}-WOF-1-reg-CR-scaled+orig

3dcalc -a '${subj}-WOF-2-reg-CR+orig' \
-b ${subj}-WOF-2-reg-CR-mean+orig \
-expr "(a/b*100)*step(b-clip level of ${subj}-WOF-2-reg-CR+orig)"
-prefix ${subj}-WOF-2-reg-CR-scaled+orig