Yes, there will be some minor differences between centos4 and centos6 
build. The differences are due to the different versions of gcc used for 
the different distributions. The centos6 build uses a newer version of 
gcc which has optimization options not available on the version gcc for 
the centos4 build, and that makes for run-time differences in recon-all.

-Zeke

On 09/26/2013 08:19 AM, Garikoitz Lerma-Usabiaga wrote:
> Hi,
> I have two identical Red Hat 6 boxes, to run recon-all-s.
>
> I just realized that in one of those I had freesurfer 5.3 for CentOS4
> and in the other one I had freesurfer 5.3 for CentOS6.
>
> I have one experiment were subjects used boxes indistinctly.
>
> According to how the software is built, should I expect different
> results among them?
>
>
> Many thanks for your help,
> Gari
>
>
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