I don't know how you (or someone else) generated the nifti files in the first place, so I can't help there. If you did not generate them, then talk to the person who did. I do not really recommend trying to do it by hand. You can get AP and SI correctly, but you'll never know whether they are LR reversed or not
On 09/11/2017 04:12 PM, Ariana Vajdi wrote: > Ah, I see - how would I be able to do either of those? And would I > have to check the geometry of each scan individually? Not sure how > that works, but I have a substantially large dataset. > > Thank you for your response! > > On Mon, Sep 11, 2017 at 1:02 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > 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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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. > > > > > _______________________________________________ > 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
