[Insight-users] [Re] Correct use of MRIBiasFieldCorrectionFilter ?

[Jisung Kim]

Hi Martin.

Thanks for clarification. I will change the ITK
documentation to include the right links. And I will
modify the Legendre polynomial to allow users to
specify subsampling. Current implementation doesn't
allow subsampling. I'm think about changing the
interator of the Legendre polynomial comply to the
specs of STL Random Iterator, so that users can use
iterator + n (unsigned int) in addition to ++iterator.
Do you think it's a valid subsampling method for the
bias correction? If so, what n would be a good default
value?

Thanks,

Jisung.
--- Martin Styner <martin_styner@ieee.org> wrote:
> Hi Christof, Jinsung
> 
> Jinsung is quite right in his answer,  but in my
> experience there 
> shouldn't be too much problems selecting the mean
> values and the 
> standard deviation values, unless the image is quite
> complex and  the 
> values are far off. The image that you provided
> seems to have only one 
> single class, is that correct? Did you model this as
> a single class 
> correction problem or did you also use the
> background as an additional 
> class? If so then you need to mask the background,
> since the background 
> should not be modeled as a class, because the bias
> field does not affect 
> the background. As single class problem, the class
> parameter values 
> should not be too sensitive (I only adjust the other
> values e.g. c_grow 
> in few exceptional cases) , but also I never used
> the bias correction in 
> images with only one class.
> Can you tell us the classes and their values that
> you chose for the 
> particular image you attached to your email?
> In regard to the use of other basis functions: It is
> not necessary to 
> use Legendre polynomials for the bias correction,
> any set of basis 
> functions should theoretically be applicable.
> Although I would suggest 
> if you try a different set of basis functions, just
> make sure to use 
> orthogonal ones (orthonormal would be even better,
> Btw, the Legendre 
> polynomials are orthogonal and not orthonormal).
> 
> When browsing through the itk-class description, I
> saw that the 
> inter-slice brightness correction is applied by
> default. In general, 
> this is actually not necessary (only for older MRI's
> it should be 
> necessary to do this). So, maybe turning off the
> inter-slice correction 
> could help.
> 
> Btw, since I am not at UNC anymore: can someone
> update the links to the 
> papers in the doxygen documentation?
> for the TMI paper: 
>
http://www.cs.unc.edu/~gerig/publications/TMI00-Styner-Bias.pdf
> for the TR: 
>
http://www.vision.ee.ethz.ch/db_queries/get_abstract.cgi?techreps:Styner97a
> 
> One more question for Jinsung: Is the itk
> implementation using 
> sub-sampling for the energy-computation? If so,
> which sub-sampling is it 
> using. I think, it would be good if one could
> actually adjust the 
> subsampling factor (in order to speed up the
> computation). Otherwise, I 
> think you did a great job with this itk-class.
> 
> Regards
> Martin
> 
> 
> Jisung Kim wrote:
> >>>Hi there,
> >>
> > 
> > Hi. I'm the person who ported the algorithm to
> ITK.
> > Martin Styner would know much better than me.
> However,
> > I will try to answer your questions.
> > 
> > 
> >>>I am using the MRIBiasFieldCorrectionFilter to
> >>>correct the bias field of a MRI 
> >>>surface coil (see attached image).
> >>
> > 
> >>>The class itself works fine, I am able to input
> and
> >>>output all the 
> >>>parameters,the image and the masks.
> >>
> > 
> >>>However, so far I was not able to obtain a good
> >>>correction. The estimated bias 
> >>>field is incorrect. So, I must be doing something
> >>>wrong. (The filter finds 
> >>>local minima instead of the global minimum).
> >>
> > 
> > It's hard to get a good result when you don't know
> > good initial statistics of the tissue classes.
> Martin
> > Styner suggested in his paper to select a small
> region
> > where pixels of all the tissue classes exist and
> then
> > pick the means of intensities values of tissue
> classes
> > in that region. Selecting the standard deviations
> for
> > the tissue classes is a little bit trickier than
> > selecting means. You can use the
> EnergyTablePlotter
> > utility that will be under the "your ITK binary
> > directory"/bin directory. you can see the usage by
> > typing the command without any commmand line
> > arguments. The utility will print energy values in
> a
> > table format. You can pipe that result to a file
> and
> > view energy function plot using mathematical
> packages
> > such as GNU R or matlab. The plot shows a good
> > separation between tissue class means. If you
> increase
> > the standard deviations, the the picks between
> tissue
> > class means would be lower. You want the picks are
> > higher than 0.5 (in energy value).
> > 
> > 
> >>>Could anybody suggest good values for cshrink,
> >>>cgrow, x0 as well as the 
> >>>coefficients for the legendre polynoms? I tried
> >>>without success the parameter 
> >>>value ranges suggested in the references.
> >>
> > 
> > I think if you have good statistics of tissue
> classes,
> > then you might get a reasonable result without
> > changing the shrink factors. However, if you want
> to
> > the optimization scheme works in a finer scales,
> use
> > smaller values.
> > 
> > 
> >>>Does anybody have experience with this filter?
> >>
> > 
> >>>Is it possible to use a basis set other than the
> >>>Legendre Polynoms (i.e. 
> >>>Gaussians?)
> >>
> > 
> > I am not sure whether current implementaion of the
> > filter works with basis functions other than
> Legendre
> > Plynoms. However, since the ITK optimization
> framework
> > expects a class that has the interfaces defined by
> the
> > SingleValuedCostFunction, it wouldn't be hard to
> use
> > other base functions. I might have to double check
> it
> > and change a little bit.
> > 
> > Thanks,
> > 
> > 
> >>>It would be a pity if this elegant correction
> >>>algorithm only worked for the 
> >>>examples given in the two references ....
> >>
> > 
> >>>Thanks
> >>
> > 
> >>>Christof
> >>
> > 
> >>>Christof Karmonik, PhD
> >>>Baylor College of Medicine/The Methodist Hospital
> >>>Mailstation M217
> >>>6565 Fannin
> >>>Houston, TX 77030
> >>>Pager: (713) 708-2232
> >>>Fax: (713) 790-4688
> >>
> > 
> > =====
> > Jisung Kim
> > bahrahm@yahoo.com
> > 106 Mason Farm Rd.
> > 129 Radiology Research Lab., CB# 7515
> > Univ. of North Carolina at Chapel Hill
> > Chapel Hill, NC 27599-7515
> 
=== message truncated ===


=====
Jisung Kim
bahrahm@yahoo.com
106 Mason Farm Rd.
129 Radiology Research Lab., CB# 7515
Univ. of North Carolina at Chapel Hill
Chapel Hill, NC 27599-7515

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