That means that geometry information (ie, what is left and right, anterior or posterior) is not part of the nifti file. Without that information, the anatomical analysis cannot be done. You will either have to fix it yourself (ie, imbed that info into the file) or, better, recreate the file with the proper geometry info
On 09/11/2017 01:52 PM, Ariana Vajdi wrote: > Hello, > > Hope this message finds you well. > > I was beginning to run recon-all on a dataset and was encountering a > problem with the talairach registration. I've encountered this error > before here and there, but I've been receiving the same error for > every scan that I've been trying to run, and I'm not sure why. It's > also the first time I've used NIFTI files as the input - not sure if > that's a contributing factor. I've also tried the -use-mritotal flag > without any luck. > > These are the errors I receive: > > WARNING: neither NIfTI-1 qform or sform are valid > > WARNING: your volume will probably be incorrectly oriented > > > ERROR: talairach_afd: Talairach Transform: > transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < > threshold=0.0050) > > Manual Talairach alignment may be necessary, or > > include the -notal-check flag to skip this test, > > making sure the -notal-check flag follows -all > > or -autorecon1 in the command string. > > > I would appreciate your help. Thank you! > > Warmly, > Ariana > > > _______________________________________________ > 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.
