[Insight-users] Fwd: How to use the class MRIBiasCorrection

[Luis Ibanez]

Hi Martin,


Several users are interested in using the MRIBiasCorrection
code in InsightApplications.


Unfortunately we are having trouble finding the papers that
are recommended in the README file.


    http://www.ia.unc.edu/public/styner/docs/tmi00.pdf
    http://www.ia.unc.edu/public/styner/docs/StynerTR97.pdf


Could you please let us know the new URL of these files ?

Google located  StynerTR97.pdf at
http://www.cs.unc.edu/~styner/public/MyPapers/thesis%20and%20reports/StynerTR97.pdf

is tmi00.pdf now at ?:
http://www.cs.unc.edu/~styner/public/MyPapers/papers/IEEE%20transactions%20on%20medical%20imaging%202000%20Styner.pdf


Please let us know,


    Thanks


        Luis


-------------------------
Oliver Trebbe wrote:
> Hi Luis,
> 
> can´t find the papers...
> 
> 404 not found
> (link broken?)
> 
> would like to have a look at them...
> 
> 
> 
> Regards
> 
> Oliver
> 
> 
> 
> Luis Ibanez schrieb:
> 
>>
>>
>> ---------- Forwarded message ----------
>> From: *Luis Ibanez* <luis.ibanez at kitware.com 
>> <mailto:luis.ibanez at kitware.com>>
>> Date: Sun, Feb 15, 2009 at 3:08 PM
>> Subject: Re: How to use the class MRIBiasCorrection
>> To: orientation f <fuzengliang435 at gmail.com 
>> <mailto:fuzengliang435 at gmail.com>>
>>
>>
>>
>> Hi Orientation f,
>>
>> Please read the REAME file in the
>>
>>      InsightApplications/MRIBiasCorrection
>>
>> and the associated papers:
>>
>>     http://www.ia.unc.edu/public/styner/docs/tmi00.pdf
>>     http://www.ia.unc.edu/public/styner/docs/StynerTR97.pdf
>>
>> If you have the BrainWeb datasets,
>>  (that you can download from
>>
>>      http://public.kitware.com/pub/itk/Data/BrainWeb/
>>
>> you can run the bias field estimator with the following command:
>>
>>  ./BiasFieldEstimator --input ~/data/BrainWeb/brainweb165a10f17.mha 
>> --class-mean 80  130 --class-sigma 10 10 --use-log yes --input-mask 
>> brainMask.mha --degree 1 --grow 1.01 --shrink 0.95 --max-iteration 
>> 20000 --init-step-size 0.1 --schedule 2 2 2
>>
>> The brainMask.mha image can be generated by thresholding the input image
>>
>> brainweb165a10f17.mha with a threshold of 80, in order to get a binary 
>> mask
>> that roughly covers the brain.
>>
>>
>> This will produce a list of coefficients as output,
>> for example, I get the following output:
>>
>>
>> Loading images...
>> Images loaded.
>> Setting multires schedule :1
>> Estimating the bias field...
>> --input /home/ibanez/data/BrainWeb/brainweb165a10f17.mha --input-mask 
>> brainMask.mha --class-mean 80 130 --class-sigma 10 10 --use-log yes  
>> --degree 1 --grow 1.01 --shrink 0.95 --volume-max-iteration 20 
>> --inter-slice-max-iteration 4000 --init-step-size 0.1 --coefficients 
>> 0.00383953 0.000627722 0.00206439 0.00339799
>>
>>
>> You can then take the list of coefficients and use them as input
>> to the ImageCorrector tool, with a command like the following:
>>
>> ./ImageCorrector --input 
>> /home/ibanez/data/BrainWeb/brainweb165a10f17.mha --output 
>> correctedImage.mha --degree 1 --use-log yes --coefficients 0.00383953 
>> 0.000627722 0.00206439 0.00339799
>>
>>
>> which will give you a corrected image.
>>
>>
>> Please not that here, for simplicity I'm using only a polynomial of 
>> degree 1
>> (e.g. a linear function.), In practice you may want to use degree = 3.
>>
>>
>>     Regards,
>>
>>
>>           Luis
>>
>>
>> -------------------------------------------------------------------------------------------------------- 
>>
>>
>> On Thu, Dec 25, 2008 at 3:31 AM, orientation f 
>> <fuzengliang435 at gmail.com <mailto:fuzengliang435 at gmail.com>> wrote:
>>
>>     Hi,
>>     I want to use the class MRIBiasCorrection for knee MR image
>>     inhomogeneity correction. But the class includes so many methods
>>     which confuse me about how to use it for correction. So, is there
>>     any instruction( as the ITK Software Guide for some class) for
>>     this class usage?
>>     Thanks a lot
>>
>>
>>
>> ------------------------------------------------------------------------
>>
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