Hi Rick,
Thanks for the quick response!
I tried warping the anat to match the EPI which worked but, although much easier and quicker, it reduces the image resolution which is not desirable for the ROI approach that I am taking. So I added the -master option using the EPI dataset as a grid and this works if I use it after motion correction. However I noticed that a previous post stated that 3dAllineate with the -EPI option (which I am doing) should be run before motion correction. Yet, when I try to run 2dImReg and 3dvolreg on the aligned EPI data I receive the following error:

++ 2dImReg: AFNI version=AFNI_2007_05_29_1644 (Sep 28 2007) [64-bit]
Choleski factorization failure in startup_lsqfit
mri_startup_lsqfit: bad call to startup_lsqfit!
Choleski factorization failure in startup_lsqfit
mri_startup_lsqfit: bad call to startup_lsqfit!

Fatal Signal 11 (SIGSEGV) received
2dImReg main
Bottom of Debug Stack
** AFNI version = AFNI_2007_05_29_1644 Compile date = Sep 28 2007
** Program Abort **
++ 3dvolreg: AFNI version=AFNI_2007_05_29_1644 (Sep 28 2007) [64-bit]
++ Authored by: RW Cox
++ Notice: -clipit is now the default
** Can't open dataset Eng.C01.series1.2dreg+orig

Is it ok to for me to run 3dAllienate with -EPI option after the data has been motion corrected? Or is there a way to solve the problem that I am having trying to run 2dImReg and 3dvolreg on the aligned EPI data?

Thanks,
Kristen