Hi Rick and Daniel,

Thank you for your response. I will definitely give afni_proc.py a try. I read the documentation online but before writing the scripts, I was wondering what the optimal way (sequence order) to preprocess my data. In a previous post, I mentioned that we had EPIs from two different sessions and we wanted to align everything together. Daniel suggested that I used the high resolution anatomical from the first session to align all the scans together (including the EPIs from the second session). However, I would also like to obtain the motion parameters for each run to include them later as regressors of no interest. So my question is:

Is it better to align all the EPIs to each other first and then use the volume registered EPIs and align them to the anatomical scan using align_e2a command

or do I align the EPIs to the anatomical scan first and then use the volreg option to get the motion parameters.

Thank you for your help,

Isa