<br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Luis Ibanez</b> <span dir="ltr"><<a href="mailto:luis.ibanez@kitware.com">luis.ibanez@kitware.com</a>></span><br>
Date: Sun, Feb 15, 2009 at 3:08 PM<br>Subject: Re: How to use the class MRIBiasCorrection<br>To: orientation f <<a href="mailto:fuzengliang435@gmail.com">fuzengliang435@gmail.com</a>><br><br><br><br>Hi Orientation f,<br>
<br>Please read the REAME file in the<br><br> InsightApplications/MRIBiasCorrection<br><br>and the associated papers:<br><br> <a href="http://www.ia.unc.edu/public/styner/docs/tmi00.pdf" target="_blank">http://www.ia.unc.edu/public/styner/docs/tmi00.pdf</a><br>
<a href="http://www.ia.unc.edu/public/styner/docs/StynerTR97.pdf" target="_blank">http://www.ia.unc.edu/public/styner/docs/StynerTR97.pdf</a><br><br>If you have the BrainWeb datasets,<br> (that you can download from<br>
<br> <a href="http://public.kitware.com/pub/itk/Data/BrainWeb/" target="_blank">http://public.kitware.com/pub/itk/Data/BrainWeb/</a><br>
<br>you can run the bias field estimator with the following command:<br><br> ./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<br>
<br>The brainMask.mha image can be generated by thresholding the input image <br><br>brainweb165a10f17.mha with a threshold of 80, in order to get a binary mask<br>that roughly covers the brain.<br><br><br>This will produce a list of coefficients as output, <br>
for example, I get the following output:<br><br><br>Loading images...<br>Images loaded.<br>Setting multires schedule :1<br>Estimating the bias field...<br>--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 <br>
<br><br>You can then take the list of coefficients and use them as input<br>to the ImageCorrector tool, with a command like the following:<br><br>./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<br>
<br><br>which will give you a corrected image.<br><br><br>Please not that here, for simplicity I'm using only a polynomial of degree 1<br>(e.g. a linear function.), In practice you may want to use degree = 3.<br><br>
<br>
Regards,<br><br><br> Luis<br><br><br>--------------------------------------------------------------------------------------------------------<div><div></div><div class="Wj3C7c"><br><div class="gmail_quote">On Thu, Dec 25, 2008 at 3:31 AM, orientation f <span dir="ltr"><<a href="mailto:fuzengliang435@gmail.com" target="_blank">fuzengliang435@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>Hi,</div>
<div>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?</div>
<div>Thanks a lot</div>
</blockquote></div><br>
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