Hi Carolina,

yes, it seems like you do have all output files. However, may I ask why you have the following files? These seem not to be the output of the scripts, as they should be rest_res.nii.gz and rest_res2standard.nii.gz

rest-res.nii.gz, rest1_res2standard.nii.gz

The best way to process several scans is to setup your directory structure like this:
subject1/anat/mprage.nii.gz
subject1/rest1/rest.nii.gz
subject1/rest2/rest.nii.gz
subject1/rest3/rest.nii.gz

That way you only have to adjust the scripts to accept restX as your func_dir, while everything else will stay the same. This will also prevent that preprocessed files belonging to different rest scans get mixed up the same folder.

Regarding the other errors: It seems the mprage and rest2 are not complete. Did they copy over correctly?

data bytes needed = 262144
data bytes input = 193507
number missing = 68637 (set to 0)

Means the file is not completely written by whatever you did before.

Maarten