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
Melbourne Neuropsychiatry Centre