Hi, 

I'm using the Connectome scripts for preprocessing individual participant resting state data using the standard method in the scripts (scripts 1 -5). After looking at the output (rest_res2standard.nii.gz) I've noticed there are large holes in the functional volumes for each participant and these holes appear to occur randomly (please see attached images). The data come from lesioned stroke patients, however the holes aren't where the lesions are. 

 Additionally the background intensity value appears to be standardised to a value of 100 which is making deriving a brain mask for later analysis difficult to say the least. 

1. Any ideas what may be causing the holes? I've used fresh copies of the preprocessing scripts in case they've been altered without my knowing and gotten data preprocessed on a colleague's computer, however the problem still persists. 

2. Is there an option to change the background image intensity?

Any help would be greatly appreciated, 

Thanks, 

Peter