Hi Carolina,

It is always a good idea to consult the AFNI ( http://afni.nimh.nih.gov/) and FSL (http://www.fmrib.ox.ac.uk/fsl/) message boards - as those are the programs that are used in all of the INDI scripts.
Familiarity with those programs will greatly aid your ability to use the scripts and understand the outputs.

http://afni.nimh.nih.gov/afni/community/...
https://www.jiscmail.ac.uk/cgi-bin/webad...

For example, a search for "spherical" on the AFNI messageboard brings me to this post:
http://afni.nimh.nih.gov/afni/community/...
Searching for the term "ROI" leads to an entire PDF on the topic:
http://afni.nimh.nih.gov/afni/community/...

Similarly, the same search on the FSL message board turns up many posts including this one:
https://www.jiscmail.ac.uk/cgi-bin/webad...

Cheers,
Clare