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

[Oliver Trebbe]

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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>
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-- 
Oliver Trebbe
Department of Neurology
University of Muenster
48129 Muenster, Germany