With distinct fields/gradients and FS 4.01 I think you can have quite distinct results. My guess: 10% difference. 

Bruce can give you a more accurate figure.

At http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes notice: "-norandomness is the the default. The binaries in the recon-all stream which are subject to variability due to usage of a random number generator (mris_smooth, mris_sphere, mris_topology_fixer, mris_topo_fixer and mris_ca_label) are now seeded with the same number, with the result being that repeated runs of the recon-all stream on a subject on the same platform will always give identical results. The -randomness flag can be used to allow usage of a random seed."

I suggest you to upgrade to 4.5.0

cheers

----------------------------------------------------------
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- For mobile: http://www.netfilter.com.br/mobile




2010/6/10 <blazey@artsci.wustl.edu>
One scanner is a Siemens Vision 1.5T and the other is a Siemens Trio 3T.
We used FreeSurfer 4.01 for the cross-sectional processing.

Thanks,

- Tyler

> It's hard to know without the info about scanner type
> (Manufacturer/Field/Sequence) and FreeSurfer version.
>
> I usually see 3-5% difference in measurements. Phillips 3T with common
> fSPGR.
> ----------------------------------------------------------
> Pedro Paulo de M. Oliveira Junior
> Diretor de Operações
> Netfilter & SpeedComm Telecom
> -- For mobile: http://www.netfilter.com.br/mobile
>
>
>
>
> On Thu, Jun 10, 2010 at 12:03, <blazey@artsci.wustl.edu> wrote:
>
>> Hi All,
>>
>> Our group recently scanned subjects with two different scanners in order
>> to determine how reliable FreeSurfer comparisons between the two
>> scanners
>> are. After putting each session through the regular cross-sectional
>> Freesurfer pipeline, we noticed that there is much greater variability
>> between the two scanners when we compare structures in the right
>> hemisphere than in the left. Is there any FreeSurfer related reason for
>> this?
>>
>> Also, we are currently running each subject through the longitudinal
>> pipeline (i.e. Scanner 1 as TP1, Scanner 2 as TP2). Is there any reason
>> to
>> think that this will help reduce the variability seen between the two
>> scanners?
>>
>> Thanks in advance for any help.
>>
>> - Tyler Blazey
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 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 . 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.
>>
>>
>