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.