Ok - thank you! I will speak to the person who generated the files then. On Mon, Sep 11, 2017 at 1:56 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:
> 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:freesur...@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 >
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