Dear FSers I extracted left thalamus as ROI volume from aseg.mgz by this command: mri_binarize --i control001/mri/aseg.mgz --match 10 --o control001/roi/l_thal.nii I overlaid l_thal.nii to control001.nii in MRIcro software in a Macbook and it looks well. However, when I overlaid l_thal.nii to control001.nii in Windows MRIcro, it comes a Warning: this NIFTI image includes an rotation transformation. When I open these two files same time, the left thalamus mismatch obviously to original T1 image. I attached an image to show my problem. I try to register this ROI volume to diffusion B0 image, and the registered left thalamus appears in the same wrong position as shown in attached image. Could someone tell me what’s wrong and how to solve it.
Regards Cong
