How do you know that the structural is left-right reversed? Or that the fMRI is? How did you create the nifti files?
On 08/16/2016 01:41 PM, Afzal, Afsana wrote: > 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 > <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 > > > > ______________________________ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
