preprocessing the task fMRI data in the human connectome project using afni_proc.py

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Hi AFNI experts and users,
When trying to preprocess task fMRI data in the human connectome, I encountered a problem. There were two runs for each task. The one run was acquired with right-to-left phase encoding, and a second run with left-to-right phase encoding (in-plane FOV [field of view] rotation obtained by inverting both the RO [readout] and PE [phase encoding] gradient polarity). So, how to combine two phase encoding runs in the preprocessing, e.g. afni_proc.py?
Thanks very much.
Rujing

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Hi Rujing,

As of now, afni_proc.py would not be able to fully process such data. It is set up to handle one or more time points in the reverse direction, but not actual data that would be part of the regression.

It also isn’t clear to me why this might be a good idea. What is done in the case of 4 or more runs, do they alternate?

  • rick