Dear Freesurfer developers,
I have a few analyse images which are oriented incorrectly
that are part of a larger dataset. When viewed in tkmedit, what is supposed to
be coronal is actually displayed as axial and the sagittal is flipped. In these
cases the Talairach transform fails spectacularly.
To try and fix the problem I used mri_info to determine the
orientation information of my good files (LSA) and of the ones that aren’t
working (LAS), then used mri_convert with the --in_orientation and out_orientation
flags to change the dimensions in analyse format. The analyze images look fine
in MRIcro and the orig.mgz looks fine in tkmedit, but yet again the Talairach
fails in the same way. I’ve also tried this by reorienting the images
using MRIcro but this has the same result.
When you view the analyze images using GWRaw MRI viewer http://www.wideman-one.com/gw/brain/orientation/orientterms.htm
(supposed to read the image file without header information), they look the
same, but I’m a bit unsure of this program.
I’m really at a bit of a loss to try and fix this
problem now so any help or suggestions would be really appreciated!
Many thanks,
Dominic