Hi,

I'm having trouble co-registering a bunch of subjects whose T1 is left-right reversed. While the orientation of the structural file in the NIfTI header is LIA and the orientation of the functional volume is LAS, visual inspection shows that the structural is left-right reversed. I then followed the steps outlined in https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal to rerun the reconstruction and re-registered the subject but the registration mincost value is still hovering around 0.9 even with the left-right reversed structural.

I've tried running registration with SPM and FSL; neither method is able to register these subjects properly.

With --init-fsl I get the following:
WARNING: initial G-W contrast is negative, but expecting positive.
If the mov data has a T1 contrast, re-run with --T1

and with --init-spm I get:
WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
 ... continuing.

At this point I'm out of ideas to try out. This issue is occurring for over 170 subjects (data collected outside Martinos using non-siemens scanners).

Any help would be much appreciated!

Thanks,

Afsana