Hi,
I am very new to AFNI and am trying out 3dAllienate but running into a few problems.
I need to coregister EPI (4 runs) to anatomical. I first tried coregistering the concatenated EPI data set (over 800 subbricks) but ran into a malloc error. So I tried to coregister one run at a time (209 subbricks) using the following script:
set subject = C01
set study = Eng

3dSkullStrip -input ${study}.${subject}.anat+orig -prefix ${study}.${subject}.anat.stripped

3dAllineate -base ${study}.${subject}.anat.stripped+orig -source ${study}.${subject}.series1.3dreg+orig -EPI -prefix ${study}.${subject}.series1.aligned

end

I have enough memory for this but run into a different error: Filesize limit exceeded.

Is there any other way that I can coregister the EPI to the anatomical? (Maybe extract one subbrick from the EPI series to use with 3dAllineate and then apply the transformations to all of the EPI subbricks?)
After coregistration, I will need to concatenate all runs and run 3dDeconvolve. Also, I need to keep the anatomical image untransformed as I will be exporting it from AFNI to draw ROIs and then bringing it back into AFNI to run 3dmaskave to get IRF for all ROIs.

Thanks for your help,
Kristen