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Hi, I am trying to register an ROI created in standard space to individual subject space and find that they are considerably displaced. As an illustration, I have defined a random ROI around then ventricles on the standard image. I then used the following command to transform it to subject space (based on the parameters from earlier first level registration). Flirt -in roi_standard.nii.gz -ref example_func.nii.gz -applyxfm -init standard2example_func.mat -out roi_subject.nii.gz. I have attached the original ROI overlay on standard image and the transformed overlay on the subject's example_func image. As you can see, the transformed ROI is considerably displaced. Any ideas what I may be doing wrong here? The original registrations at the first level look fine. Thanks Vinod PS: I have also applied flirt as a two stage process going from standard to highres and then from highres to functional and results look the same.