3dSatCheck Tool

Hello AFNI Experts - I have been looking over 3dDeconvolve documentation and noticed the mention of a tool called 3dSatCheck. However, I have found little recent documentation on its functions. As well, it was not included in my recent download of AFNI.

Is this tool deprecated in favor of something else?

3dSatCheck exists, but is not compiled in AFNI binary distributions. I’m not sure it is particularly useful. At the moment I wrote it, my idea was that people would need a way to check for pre-steady state in their data. However, my love for this idea waned quickly, as I now feel that people should LOOK at their data to get an idea of how much pre-steady state (pre-saturation) artifact is present at the start of each imaging run. If you have a study with all data acquired under the same scanning protocol, all EPI datasets should be pretty much the same in this regard.

3dSatCheck -help output

Sample run:

I second that vote for looking at the raw EPI data to see whether it contains uniformly high early values.

It might also be worth noting that this is also a feature afni_proc.py will try to check for and warn users about; it plops any potential warning in an output text file called “out.pre_ss_warn.txt”, and this datum is also displayed (and potentially flagged) and the QC HTML that afni_proc.py creates.

But again, looking at the data initially is certainly the best way to start.


Hi All - Thank you! This is helpful!