Yes they are just warning and can be ignored. The upcoming release of 
freesurfer v6 has addressed the deprecation issue.

-Zeke

On 06/23/2016 11:48 AM, Rockers, Elijah D. wrote:
> Hello,
>
> Doing a recon-all -all yields some deprecation warnings.
>
> defined(@array) is deprecated at
> /freesurfer/mni/bin/nu_estimate_np_and_em line 165.
>
> Use of ?PATTERN? without explicit operator is deprecated at
> /freesurfer/mni/bin/sharpen_volume line 153.
>
> I think my results should still be OK because it's a warning, but I just
> wanted to make sure.
>
> Thanks,
>
> Eli
>
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