Hi Xiaozhen,
The Conn toolbox uses the ART Artifact Detection Toolbox, which computes regressor files for outliers and movement. To my knowledge, the scrubbing you're referring to (i.e., throwing out bad time points altogether), is implemented in a different toolbox with a similar name, that is, the ArtRepair toolbox from Stanford (http://cibsr.stanford.edu/tools/human-br...).
The reason why it is advised to use regression rather than removing outlier time points, is because you want to maintain the temporal resolution of the data. By removing time points, you're altering the length of scans, making some longer than others, for better or worse (though I'm under the impression it is for worse).

It would be nice if you could run both analyses, and tell us what you find. We did something similar: We looked at analysis results using the ART outlier regressors and no despiking, using art regressors and 'despiking', not using outlier regressors and not using despiking, and not using outlier regressors but using despiking. We're still under the process of finishing the comparisons.

All the best,

Fred

Originally posted by Xiaozhen You: