I'm not sure about the mri_robust_template issue, but you can check the orientation by loading it in tkmedit. If the axial is axial with (nose up) and the sag is sag (with nose to the right), then the qform is right (assuming that LR is ok, which you can't check based on the direction of the nose:). doug
Nikolas Borrel-Jensen wrote:
Hi!
I am having some trouble with the motion correction step when having two volumes (NIFTI files). The average volume has not been determined correctly due to a wrong orientation/registration of the two original volumes (see http://freesurfer.nikolasborrel.com/bad_registration.tif). Is the problem caused by wrong information in the qform matrix in the header of the NIFTI file or by a bad registration in the mri_robust_template or mri_convert functions in the motion correction step?
Kind regards Nikolas Borrel-Jensen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer