On Mon, Sep 11, 2017 at 1:56 PM, Douglas N Greve <greve@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

> <greve@nmr.mgh.harvard.edu <mailto:greve@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
> >
> >
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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