Alfonso,

My apologies for not responding back sooner. I was side tracked on some other projects. With the summer here I am trying to get back to this.  I made the suggestion that you made but it didn't remove the warning. The warnings were  created during the Step 5/7 Importing ROI data. I am creating a new project from scratch. I am using data that has been preprocessed through the CONN toolbox as individual projects. I wanted to merge the projects but they were not processed identically due to human error.   

Can you explain to me what the error messages mean?

When I posted the original question I was having problems moving to the First Level Analysis. I was told that Conditions weren't loading. I was trying to track down the problem and started with the Warning Messages. I am not longer encountering problems with the first level analysis so I will just move one. I guess the take away messsage is if you wait long enough problems will resolve themselves. 

Thanks for your help,

Bob