Re: [Freesurfer] Orientation

[Doug Greve]

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 CONFIDENTIALITY NOTICE This message is confidential, intended only for the named recipient(s) and may contain information that is privileged, or exempt from disclosure under applicable law. If you are not the intended recipient(s), you are notified that the dissemination, distribution or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the e-mail address. Delete this e-mail from your computer, and destroy any copies in any form immediately. Thank you.     _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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