Hi - there's a number of things that can have changed in your scanner
upgrade that could cause this, including intensity effects and
geometrical effects.
In general we _strongly_ recommend against any acquisition changes
during a longitudinal study, as you can never be sure that you will be
able to remove the confounds caused by the change.
In your case you will need to look into all the intermediate stages
(outputs) of SIENA to try to track down where this confound is
affecting estimates. If you use the -d debug option SIENA will leave
a lot of intermediate stages for you to look at.
Cheers.
On 5 Sep 2009, at 08:20, Mehul Sampat wrote:
> Hi FSL Experts,
>
> I am using Siena to compute PBVC for MS patients.
> In the past we would see a mean -0.4% PBVC value for two scans a
> year apart.
>
> Recently, our GE scanner went through a software upgrade.
> I am now comparing two scans (pre- and post- upgrade) using Siena.
> (These pre- and post-upgrade images are also a year apart)
> Strangely for many of the subjects, the PBVC values are now positive
> (which is not what we expect for these patients).
>
> I tried Siena version 2.6 and version 2.4 and for both versions I see
> positive PBVC value.
> Has anyone experienced similar issues with Siena ? If so any
> suggestions to overcome this issue would be very helpful.
>
> Also any suggestions on debugging the intermediate steps would also be
> very helpful.
> Thank you,
> Mehul
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
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