Hi Dominic the big problem is that you'll never know if you have a left/right swap.
sorry :< Bruce On Tue, 3 Nov 2009, Dominic Brendon Dwyer wrote: > Hi Bruce, > > Thanks for your quick reply. Unfortunately the images are more than 10 > years old and have only been stored on our systems in analyze format. > I'm trying to source the original DAT tapes, but thought I'd try to fix > the problem without them. In the main I was puzzled that tkmedit reads > the converted image ok, but the talairach fails as if the orientation > information was still wrong. If there are other things I could try it > would be great to know, otherwise I'll just cross my fingers and hope > for the tapes. > > Thanks very much. > > Dominic > > > -----Original Message----- > From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] > Sent: Monday, 2 November 2009 11:20 PM > To: Dominic Brendon Dwyer > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] orientation problem resulting in talairach > failure > > 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
