Hi Jamie,

Yes, you can use the toolbox just for preprocessing, and you had the right idea to just use the functional brain mask for both the brainmask and ROI mask fields. 

I think what might be going wrong is how the participant IDs are entered.  Basically, there you just want to have the part of the filename that changes with each participant (so not having '_rest.nii.z' for example).  So, if you have three participants and the files were named something like:

101_rest.nii.gz
102_rest.nii.gz
103_rest.nii.gz

the cell array would be:

Subjects = {'101';'102';'103'};

(i.e., run that on the command line, then put Subjects in the appropriate field)

Also, for the array of ROI labels use this:

labels = {'wholebrain',1};

This is just telling the script that there is only one ROI, and the value of that ROI in each 3d ROI file = 1.