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