(Reply also contains the answer to your email query: "I also want to know the basic algorithm behind "3dSkullStrip" as in AFNI's original paper I did not find it in a clear way. ")

All I have as written description is in the first few lines of the -help output. You need to be a lot more specific about your question regarding "Performing noise removal". There are options for spatialsmoothing but they are not default. Any attempt at making an algorithm robust involve some desensitization to noise and there is plenty of that in the heuristics of the algorithm.

Some bias field correction is carried out in the preprocessing stages. But when you ask for orig_vol or mask_vol, any corrections are not applied in the output.

cheers
ziad