Unfortunately, I don't think FTIR is a good technique for that particular case. OH bands tend to be quite broad and so distinguishing between -OH groups and water would be very difficult indeed!
You won't be able to determine much of use with OH stretching frequency however there are other modes that may be useful depending on what the OH is attached to.
Ofcourse, FT-IR is a powerful tool when the sample is free from moisture. In your case, you can easily distinguish OH stretching frequency and OH frequency of water. For free OH, the stretching frequency is usually observed in the region 3550 - 3650 cm-1. Suppose when the bond involves hydrogen bonding, it will be observed in the region 3200-3300cm-1. So you can distinguish both the frequencies.