Re question 1:

We strongly encourage you to use only one motion correction method when analyzing your data. You can try different methods, one at a time, to visualize the impact it has on your data. But at the end, choose only one to use.

Re question 2:

You really should use the same processing stream and function parameters for all subjects. Tailoring your processing stream functions and parameters to get the "optimal" result for each run means that you are introducing your own subjective bias into the analysis to get the result you want.

Re question 3:

This is why we have "apply all" checked, to make sure you use the same processing parameters for all subjects. Of course, you can uncheck this and then "optimize" parameters for each subject. But then you are at risk for producing the results you want to see. This can easily bias the results of your study to achieve your expected result.

Lisa raised several general questions about correcting MA as discussed in Day 4 of the fnirs course 2020.