Dear list, I am using mri_convert to prepare my pipeline for FreeSurfer, and, yes, I have been struggling for a couple of days to get it done.
After conversion, I have no problem using tkmedit to display the file; however, the Volume RAS coordinates are swapped -- the numbers aren't wrong, they are just swapped in place and/or inverted, while the image is always displayed fine (left on the right, up is up, front is front etc, which shows, I assume, that the coordinates are right in the header). By 'always' I mean that if I reslice the image, and then convert it, then mri_convert will always produce an mgz file that will be displayed correctly in tkmedit, but will also produce a new permutation of the swapping in the Volume RAS coordinates. Even if a reslice my image in axial slices (it was originally the usual sagittal MPRAGE thing from Siemens), I get the wrong swapping. Can anyone tell me how to reslice my image to get it right? Thank you in advance, Roberto Viviani University of Ulm, Germany _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
