Hi Amy
starting with the original dicoms is usually a good idea. Bruce On Tue, 6 Aug 2013, Amy Bilderbeck wrote:
Apparently my problem is because my .nii.gz files lack any orientation data, and I?m going to see if I can get the original DICOM data to address this.
Any other tips welcome, otherwise I?ll see how far I get with that.
Best,
Amy
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Amy Bilderbeck Sent: 06 August 2013 14:44 To: 'freesurfer@nmr.mgh.harvard.edu' Subject: [Freesurfer] output orientations wrong
Dear FreeSurfer community,
I?ve been unable to get my recon-all commands to work, and this appears to be because my output orientations are wrong.
As input, I am using .nii.gz structural images (from 3 different scanners: a Siemens Sonata (1.5T), Siemens Trio (3T) GE Signa (1.5T))
Using FSLview, I?ve looked at the input structural images and I believe my input orientations are all fine and consistent across all the files. My output talairach.xfm, and orig.mgz, appear with the axial and coronal images ?swapped? (one is labelled as the other) and my saggital images appear oddly too, with the nose down.
I believe you have had reports of this problem before but I have not found a solution in my case.
Thanks and my warm regards,
Amy
Dr Amy Bilderbeck
D.Phil Experimental Psychology
Department of Psychiatry, University of Oxford