Hi Gang,

I'm doing something similar to above but was hoping for advice on questions I have.

>3dSynthesize -cbucket CbucketFileFrom3dDeconvolve+orig -matrix x1DFrom3dDeconvolve -select ... prefix EffectsOfNoInterest
>Then remove the effects of no interest from the original signal by using 3dcalc:
>3dcalc -a InputFor3Deconvolve -b EffectsOfNoInterest -expr 'a-b' -prefix CleanData

So above you subtract with 3dcalc the effects of no interest from the Input file to 3ddeconvolve. This presents an issue to me as my 3dDeconvolve actually takes 6 runs but outputs one bucket for one EffectsOfNoInterest file. See below for the portion of my code that does this.
...value=$(<../${i}/GLM_BASIC/scans.txt)
set $value
3dDeconvolve -force_TR 1.77 \
-local_times \
-input ../${i}/GLM_BASIC/$1 ../${i}/GLM_BASIC/$2 ../${i}/GLM_BASIC/$3 ../${i}/GLM_BASIC/$4 ../${i}/GLM_BASIC/$5 ../${i}/GLM_BASIC/$6 \ ...

Can I simply paste together the 6 runs, subtract the EffectsOfNoInterest, and use the output for the rest of functional connectivity steps (ex. warping, 3dmaskave for ideal file, 3dfim+, etc.)?

If so I'm not sure I understand what is going on. I thought the 3dDeconvolve models the activity for each event fed in by the StimTimesIM files. If running functional connectivity on the raw rscan files (with EffectsOfNoInterest subtracted) how is the comparison made between trial types (ex. correct trials vs incorrect trials)? The first time I did func. con. analysis (without subtracting effectsofnointerest) I used the stats output and it seemed to work as expected. Was that wrong?

Thanks for any help you can offer as this is the last obstacle for analyzing my results!

Best
Kirk