What is the original source of the images? If dicom, try loading the dicom directly into tkmedit, something like:

tkmedit -f image.dcm

Which axis is it flipped around?

Lindsay Casmaer wrote:

Hello,

After running autorecon1 and viewing the brainmask.mgz images with tkmedit, the images appear rotated 180 degrees.

Any suggestions on how this might be corrected would be greatly appreciated.

The images are Seimens 3T Trio images that were converted without errors to the mgz format.

Thanks, Lindsay

Lindsay J. Casmaer Washington University in St. Louis _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer