Hi Carolina,

yes, rest_res.nii.gz is the output (as is rest_res2standard.nii.gz). It indicates the residuals of the resting state preprocessing which included regressing out signal from white matter, CSF and the global signal. For the rest of the analyses we will be working with the residuals of that regression.

The seed_list is something you create yourself. It should contain the names of ROI's or seeds that you created and that you want to use to do a functional connectivity analysis. In such analysis you correlate the timeseries of your seed with the timeseries of all other voxels in the brain, effectively assessing how similar a voxel's fluctuations are to the fluctuations of your seed. High correlations would mean they are "functionally connected", i.e., showing the same signal fluctuations.

Take a look at this paper for a nice example:
http://dx.doi.org/10.1016/j.neuroimage.2...
NeuroImage
Volume 37, Issue 2, 15 August 2007, Pages 579-588
Mapping the functional connectivity of anterior cingulate cortex
Daniel S. Margulies, A.M. Clare Kelly, Lucina Q. Uddin, Bharat B. Biswal, F. Xavier Castellanos, and Michael P. Milham

Maarten