Hi Hazel,

If I understand correctly, you have multiple ROIs in your file that you'd like to combine into a single bilateral hypothalamus ROI. I don't think that you can do this directly in CONN, but you can do it by creating a binary version of the multiple ROI file with spm_imcalc. For example (don't type any quotes...):

1) Enter "spm_imcalc_ui" at matlab prompt
2) Select your multiple ROI file (e.g., "ROI.img")
3) Enter file name for the binary output file (e.g., "ROI_bin.img")
4) Enter evaluated function "i1>0"

Then use that new binary ROI file in CONN. Hope that helps,

Brad