Dear PT,

Thank you very much for your detailed and useful explanation! It is indeed important, needed and interesting to know those things!

However, I do not necessary and intentionally run the 3dFWHMx command, therefore I am not actually able to specify any of the options you present, so I am not able to have the output of the -ACF option saved separately (e.g. for each run a different file). In my case I want to blur the image after the preprocessing (before the 1st level analysis) using the 3dBlurToFWHM command. This command (the 3dBlurToFWHM), after is completed, somehow starts automatically the 3dFWHMx command in order to check the blurring process. As I said, since I do not intentionally run the 3dFWHMx, I do not have a full control on the command; more specifically am not able to include all the suggested option for the 3dFWHMx command. My question was, since the 3dFWHMx command is still running in this manner, is there a way to operate it's options such that those outputs (e.g. 3dFWHM.1D and 3dFWHM.1D.png) will be still saved for each run of the fMRI data?

I was thinking to one solution: since I am not able to operate the options of the 3dFWHMx command, I could save each output of each run of the 3dBlurToFWHM command (so implicitly of the 3dFWHMx command appearing automatically after the 3dBlurToFWHM command) in different folder; in this way will have the data saved using the default name (3dFWHMx.1D and 3dFWHMx.1D.png) but in different folder, so the outputs for different run of the same subject will not overlap; but maybe there are some other more professional/easy way to address this situation.

Thank you in advance for your help!

Yours sincerely,
R. Nechifor.