Hi Frances,

It sounds like your ROI is not in IIT space. To make sure the ROI is in IIT space, you can open the mean FA template (IITmean_FA.nii.gz), or the mean T1 template (IITmean_t1.nii.gz), or any other template of the IIT atlas as reference and draw the ROI based on the template you see in the background. Just make sure you use the matrix size you are interested in. The IIT atlas is available in 182x218x182 or 256x256x256; the latter templates have filenames that end with _256. Make sure you pick the matrix size you want. An ROI defined in one matrix size will not work in the other. By using an IIT template as background, you ensure that the generated ROI is located in IIT space. Please let us know if you continue having problems.

Regards,
Konstantinos