Hi Dominic, do you have access to any format previous to the analyze one? It doesn't preserve orientation info, and all bets are off once you go through it.
cheers Bruce On Mon, 2 Nov 2009, Dominic Brendon Dwyer wrote: > 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 > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
