Dear Alfonso,

Thank you for your reply! Unfortunately, the problem occurs when I select the correct analysis name.  When I select an analysis name for which the first level ROI-to-ROI results were not run, it warns me that the results have not been run.  However, when I select the analysis name for which the first level ROI-to-ROI results have been run (along with the seed-to-voxel results), it simply defaults to the Seed-to-voxel tab, rather than showing the ROI-to-ROI results.  

Additionally, for the second question, in the "explore factors" tab, the plot that appears shows factor scores for the first session, and, although an area is present denoting the second session, there are no factor scores/lines reporting the information, it simply appears blank.  (I also tried running session 2 separately (and did not select both conditions), and the first session is still the only session present.  (However, for other analyses such as voxel-to-voxel and seed-to-voxel, the second session is present/working fine.)

One thing I just noticed is that when I look in the first level results folder, there appear to be folders called "Dynamic factor _01" with folders for 01 through 10.  Inside the first folder (01) there are files called BETA_Subject#_Condition#_Source# where both conditions 001 and 002 are present for each subject (additional files in this folder include corr, p_corr, pFDR_corr, and se). The rest of the Dynamic factor folders (02-10) have different contents with files named resultsROI_Subject#_Condition#.mat where condition # is 001 and 002. I wonder if the first folder contains ROI-to-ROI information, rather than Dynamic FC information.  

One last thing of note is that the first level folder (that contains the analysis folders and the Dynamic factor folders 01-10) also contains files (not in any folder) called BETA_Subject#_Condition#_Measure#_Componenet#.nii with conditions 001 and 002, and additional files named PCAcov_Measure#_Component#.nii, and finally a mat file called TEMPORAL1_Measure001.  Is it possible that the information is all there but that the folders / files somehow got in the wrong place, or should these folders be arranged in this way?

Thank you again so much for your help on this!

Ruth