when filling in the black as you proposed, the numbers change slightly:
m00-m04: -0.1039 instead of -0.0583
m04-m06: 0.7461 instead of 0.8557
the three-step error decreases (m00-m06: 0.6687): 0.0265 instead of
Thanks for your help
Dr. Martin Hardmeier
Department of Neurology
University Hospital Basel
Tel: 0041-61-2652525; pager -2913
>>> [log in to unmask] 08/30/04 8:58 AM >>>
Indeed SIENA is tracking the temporal changes of this black hole and
that is counting towards the total PBVC. If (as is probably sensible)
want to exclude the effect of this then yes you can mask it out yourself
either before or after running SIENA. It's probably easier to do it
before, as we discussed, by using fslview to "fill in" the hole with
intensities matching the WM.
If you have done the post- corrections right, then yes I wouldn't expect
the overall results to change hugely from such a small area, though if
mean flow was close to zero already then the "%" change might be high
(synchronicity!). You could easily test your methodology by comparing
happens if you remove the hold before running SIENA.
On Sat, 28 Aug 2004, Martin Hardmeier wrote:
> Dear All,
> Using SIENA for atrophy measurements in MS, I am wondering, whether
> PBVC is influenced by acute black holes.
> In the following example an acute black hole showed up in m04 over
> 3mm slices.
> The render image showed a big change in the area of the acute black
> from m04 to m06 (see attachment).
> To evaluate the impact of this acute black hole I manually edited the
> flow images (m04-m06) and calculated the number of non-zero Pixels and
> the mean (avwstats -V -m) (see below).
> Although through editing only a small portion of the overall number of
> Px changed, the mean has changed dramatically (38,7%).
> As I understand, the mean is one factor in the calculation of the
> overall change, so this acute black hole may influence the result and
> taken as atrophy.
> How would you interpret the change in the mean flow, does it
> significantly impact the overall PBVC?
> Are there other factors accounting for these kinds of errors?
> Is there a possibility to mask such areas?
> Should such images be excluded from analysis?
> best regards
> m00_to_m04: -0.0583
> m04_to_m06: 0.8557
> m00_to_m06: 0.6687
> image # non-zero Px mean of non-zero Px
> m04-m06-flow 152475 0,000354
> m06-m04-flow 148526 -0,000528
> after editing flow images and erasing change detected in the area of
> acute black hole
> m04-m06-flow-mod 151872 0,000217
> m06-m04-flow-mod 148382 -0,000490
> difference between normal and edited images
> # Px m04-m06: 603 = 0,395%
> # Px m06-m04: 144 = 0,097%
> mean of non-zero Px m04-m06: 0,000137 = 38,7%
> mean of non-zero Px m06-m04: 0,000038 = 7,2%
> Dr. Martin Hardmeier
> Department of Neurology
> University Hospital Basel
> Petersgraben 4
> 4031 Basel
> Tel: 0041-61-2652525; pager -2913
> Fax: 0041-61-2654100
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve