Re: [Freesurfer] Talairach registration error

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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