What coordinates is your other tool using and how do you know that they are from the same coordinate system that tkmedit uses? There are many different coorindate systems (tkmedit will show two, volume and scanner).
doug
roberto.viviani@uni-ulm.de wrote:
How do you know what coordinates it should be?
Because I can open the Nifti image with something else and use anatomical landmarks to verify where I am...
Be it as it may, loading a different mgz image in tkmedit does not reset the position of the pointer, so I can easily observe the swapping of coordinates after loading a resliced volume.
Also, try looking at the scanner coordinates instead of the volume coordinates.
The 'Volume index' label giving coordinates in voxel units? After reslicement+conversion, these coordinates change, but the raw data are indeed reordered.
best, Roberto
doug
On 9/16/10 8:27 AM, roberto.viviani@uni-ulm.de wrote:
Hallo,
HI Roberto, I can't quite tell what the problem is that you are trying to fix. What is actually going wrong? If it displays correctly in tkmedit, then the coordinates are probably write. I don't know what you mean when you say the the Volume RAS coords are swapped.
I mean that when I click on a voxel that is supposed to be at coordinates x, y, z -25 10 -20, say, the Volume RAS label tells me I am at -25, -20, -10. I reslice the image (including the new mapping in the header), reconvert it, then tkmedit displays it just the same as before, but, at the same voxel, the Volume RAS coordinates are 10 -25 -20.
Thanks again, Roberto Viviani
doug
roberto.viviani@uni-ulm.de wrote:
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
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