[Insight-users] MRIBiasCorrection

[Jisung Kim]

Hi.

There was some bug fixes after 1.4 for MRIBiasField
applications. 

As you mentioned in your post, the mean and standard
deviation selection is critical to the whole process.
Even "right" statistics may not produce the right
result. In my experiments, standard deviations were
most important factor for the result. You can see the
shape of energy function resulted from your mean and
standard deviation selections using the
EnergyTablePlotter program in the binary directory. It
prints out pairs of intensity value and enery value to
standard output. You can pipe that into a file and
load the data to some graph tools (I personally used
GNU R).

In the plot, we want to see high peaks for each class
mean (over 0.5) and clear low valley between class
means. With large standard deviation, the valley would
neither be low, nor provide good separation between
class means. 

Thanks,

--- "Wang, Liqin" <Wang . Liqin at mayo . edu> wrote:
> I tried to use the sample program of
> MRIBiascorrection to correct a 8 bit MRI image
> dataset with obvious bias field. I first run
> IntensityHistogram3D with bin size of 8, then chose
> two intensity values with highest frequencies. The
> class mean and sigma were calculated for these two
> intensities ( in the range of intensity values plus
> or minus half bin size, respectively). The binary
> output mask were generated with other program and
> input mask was generated by on the basis of  output
> mask and class mean values. After running the "Bias
> field Estimator"  and "ImageCorrector", it seems
> that a wrong bias field got computed. I believe the
> calculation of class mean and sigma plays the
> critical role in this correction. Could you let me
> know where did I do wrong? How can I get the class
> mean and sigma accurately in order to get the right
> results?
> 
> Thanks,
> 
> Liqin
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=====
Jisung Kim
bahrahm at 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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