Alfonso,

I tried running realignment and unwarp without the susceptibility distortion correction, which did not fix the problem, so I think it may be an issue with the masking that occurs during realignment, like you suggested here: https://www.nitrc.org/forum/message.php?... I'd like to try to skip the masking to see if that fixes the issue, however I'm relatively new to CONN and am not yet familiar with the command line interface. Is there a way to disable masking when using the GUI?

Thanks again!
Hannah