Thank you for your reply Dr. Reuter.

I have about 3 scans in which the acquisition parameters are slightly different between time 1 and time 2 which probably contributes to these differences. Do you recommend that I do not use these scans?

For my other scans, sometimes the differences in intensity are very subtle. For example, I have one scan where the contrast between the GM and WM are more apparent at one time point vs. the other time point. In another example, the thalamus looks a bit darker at time 1 vs. time 2. Again these differences are very subtle and only noticeable if you are looking for them. I am just wondering at what point do these differences become problematic? I should also note that sometimes these differences are not readily apparent in the original T1 scan.

Thank you again for your help.

Best,

Tamara