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

[Nicholas Tustison]

Great.  I'm glad it worked for you.  Let me know if you find anything  
else.

Nick



On Oct 8, 2009, at 6:47 AM, Lassi Paavolainen wrote:

> Hi Nick,
>
> On Wed, 7 Oct 2009, Nicholas Tustison wrote:
>
>> Hi Lassi,
>>
>> Considering that you were looking at the corners, my initial  
>> suggestion was going to be to try a mask where all the voxels have  
>> a value of 1.  Let me know what that does and, based on the  
>> results, we can try different things from there.
>
> That really did the trick. Thanks Nick for all the help and for  
> implementing this nice filter.
>
> Lassi
>
>> On Oct 7, 2009, at 6:18 PM, Lassi Paavolainen wrote:
>>
>>> Hi Nick,
>>> On Wed, 7 Oct 2009, Nick Tustison wrote:
>>>> 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?
>>> Ok. I explained it badly. This example dataset has its brightest  
>>> illumination in lower left area of the image. Average intensities  
>>> then go lower to the upper part of the image and to the right part  
>>> of the image. Its some sort of Gaussian distribution where the  
>>> center is in lower left part of the image. I measured those  
>>> average intensities by calculating mean of area about 512x512 in  
>>> five different places (left-top, right-top, center, right-bottom,  
>>> left-bottom).
>>> Even though mask image is said not to be that important, could it  
>>> be the solution for this problem? In this case using Otsu just  
>>> masks upper right part of the image and elsewhere some noisy parts  
>>> of the data. At least this mask image is quite different of what  
>>> you would expect to get from MRI data. I tested bias correction in  
>>> EM data.
>>> Lassi
>>>> 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
>>>>
>>>>          _____________________________________
>>>>          Powered by www.kitware.com
>>>>
>>>>          Visit other Kitware open-source projects at
>>>>          http://www.kitware.com/opensource/opensource.html
>>>>
>>>>          Please keep messages on-topic and check the
>>>>          ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>>          Follow this link to subscribe/unsubscribe:
>>>>          http://www.itk.org/mailman/listinfo/insight-users
>>>> --
>>>> Lassi Paavolainen, M.Sc.
>>>> Software Engineer
>>>> BioImageXD (http://www.bioimagexd.net)
>>>> lassi.paavolainen at jyu.fi
>>> -- 
>>> Lassi Paavolainen, M.Sc.
>>> Software Engineer
>>> BioImageXD (http://www.bioimagexd.net)
>>> lassi.paavolainen at jyu.fi_____________________________________
>>> Powered by www.kitware.com
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>> Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ
>>> Follow this link to subscribe/unsubscribe:
>>> http://www.itk.org/mailman/listinfo/insight-users
>>
>
> -- 
> Lassi Paavolainen, M.Sc.
> Software Engineer
> BioImageXD (http://www.bioimagexd.net)
> lassi.paavolainen at jyu.fi