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

[Luis Ibanez]

---------- Forwarded message ----------
From: Luis Ibanez <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>



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


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On Thu, Dec 25, 2008 at 3:31 AM, orientation f <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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