[Insight-users] Correction of non-uniform illumination in EM data

[Nick Tustison]

Hi Lassi,

In general, inspection of the corners in an image probably does not
constitute a proper assessment of bias correction algorithms.  Can you
describe your data a little more and perhaps I can point you to some
variations you might want to try?
Nick


On Wed, Oct 7, 2009 at 8:46 AM, Lassi Paavolainen
<lassi.paavolainen at jyu.fi>wrote:

> Hi Nick,
>
> On Thu, 24 Sep 2009, Nicholas Tustison wrote:
>
>  Hi Lassi,
>>
>> You might want to take a look at the N3 algorithm implemented in ITK.  It
>> might provide what you're looking for.
>>
>> http://www.midasjournal.org/browse/publication/640
>>
>> Good luck,
>> Nick
>>
>
> I have played around with that now. It looks promising but doesn't do its
> job completely. I have tested it with one dataset where mean intensity is
> around 130 in lower left corner and around 100 in upper right corner.
>
> When I run test program from your publication using shrinkFactor = 4 and
> using default iteration number and number of fitting levels values, I get
> image where difference between those areas is about 20. Running it five
> times difference is subtracted to around 10. I have changed the number of
> iterations and fitting levels without making a much of a difference in
> results.
>
> So it looks really promising but I would like to get the job done by
> running it only once. Of course results cannot be perfect (there is no
> perfect solution in image analysis). Do you have any idea where I should
> look into to make it converge to some sort of optimal result by running the
> filter just once?
>
> Lassi
>
>
>  On Sep 24, 2009, at 4:23 AM, Lassi Paavolainen wrote:
>>
>>  Hi,
>>>
>>> Does anyone know about ITK method to correct non-uniform illumination?
>>> There seems to be MRIBiasCorrection class and an example of it in
>>> InsightApplications. I'm not sure if this class can help me and anyway it
>>> doesn't seem to be very easy to use.
>>>
>>> I have read following technical report (
>>> www.sci.utah.edu/~tolga/pubs/UUSCI-2005-008.pdf). One of the authors
>>> seems to be Ross Whitaker who is involved in ITK too. Is there ITK
>>> implementation of that method?
>>>
>>> Lassi
>>>
>>> --
>>> Lassi Paavolainen, M.Sc.
>>> Software Engineer
>>> BioImageXD (http://www.bioimagexd.net)
>>> lassi.paavolainen at jyu.fi
>>>
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>>
>>
> --
> Lassi Paavolainen, M.Sc.
> Software Engineer
> BioImageXD (http://www.bioimagexd.net)
> lassi.paavolainen at jyu.fi
>
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