Hi Paul,

Thank you again for your response! Do you mind if I ask a few related questions please?
I ran the command
3dRSFC -prefix RSFC 0.01 0.1 data.nii.gz
and I got these files:
RSFC_ALFF+orig.BRIK, RSFC_mALFF+orig.BRIK, RSFC_fALFF+orig.BRIK, RSFC_RSFA+orig.BRIK, RSFC_mRSFA+orig.BRIK, RSFC_fRSFA+orig.BRIK (and the corresponding HEAD files).

1 - I'm confused about the -no_rs_out option. In the help file it says this doesn't output the processed time series, which I assume is outputed by default. However running the program without this option does not output any other file apart from the ones I mention above. In fact I ran the command above with and without this option but the result is the same (so omitting this flag does not change any of the outputs nor create new outputs).

2 - You say that there is an option to output the bandpassed data, but the only option I found in the help file was the -un_bp_out which outputs the un-bandpassed filter. Is there another option that I can define to output the bandpassed time series?

3 -The idea is to run 3dRSFC after motion correction and perform detrending and orts in one go with either 3dRSFC or 3dTProject. My question is whether it makes a difference whether I use the -ort option in 3dRSFC or 3dTProject? Or are they equivalent?

Thank you very much in advance!

Best regards,
Sam