Is the orig.mgz oriented correctly? How about the rawavg.mgz and the orig/001.mgz?
Dick, Rachel wrote:
Hello all,
I have been using Freesurfer for quite some time. However, I have run into a problem. I am using a properly oriented input image (just like all others I have used before), but when I go to look at the brainmask.mgz after autorecon1, the image is flipped on the y axis. I have used mri_convert -out_orientation to change it and also the FSL tool avwswapdim to change the orientation but it doesn't make any difference. Once I open it in Freesurfer, it is always flipped along the y. Please help!!
Thanks in advance.
Rachel Marie Dick
Research Assistant/Coordinator
Brain Research and Imaging Neurosciences
Dept. of Psychiatry & Behavioral Neuroscience
WSU Medical School
brain.wayne.edu
(313)577-6279
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