<br>Hi Xavier,<br><br>You probably already read the papers that describe this method:<br><br><a href="http://public.kitware.com/Insight/Doxygen/html/classitk_1_1MRIBiasFieldCorrectionFilter.html">http://public.kitware.com/Insight/Doxygen/html/classitk_1_1MRIBiasFieldCorrectionFilter.html
</a><br><br><p> "Parametric estimate of intensity inhomogeneities applied to MRI" <br>Martin Styner, Guido Gerig, Christian Brechbuehler, Gabor Szekely,<br>IEEE
TRANSACTIONS ON MEDICAL IMAGING; 19(3), pp. 153-165, 2000,</p><p> (<a href="http://www.cs.unc.edu/%7Estyner/docs/tmi00.pdf">http://www.cs.unc.edu/~styner/docs/tmi00.pdf</a>)</p><p>
"Evaluation of 2D/3D bias correction with 1+1ES-optimization" <br></p><p>Martin
Styner, Prof. Dr. G. Gerig (IKT, BIWI, ETH Zuerich), TR-197 <br></p><p>(<a href="http://www.cs.unc.edu/%7Estyner/docs/StynerTR97.pdf">http://www.cs.unc.edu/~styner/docs/StynerTR97.pdf</a>)
</p><br><br>As you have seen from the papers, the method combines a segmentation <br>process with a bias field correction process.<br><br>That lead to several questions:<br><br>1) Is the MRI image that you are segmenting, an image of the Brain ?
<br> if not, you must rethink the number of classes, initial means and <br> sigmas that will correspond to the Gaussian mixture model of the<br> tissues present in your image.<br><br>2) Have you manually evaluated the mean intensity values of the
<br> tissues present in your image ?<br> <br> Have you compared those values to the means of the Gaussian<br> distributions that this method is fitting to the histogram ?<br><br><br><br><br> Regards,<br><br><br> Luis
<br><br><br>-----------------------------------------------------------------------------<br><div><span class="gmail_quote">On 3/26/07, <b class="gmail_sendername">Xavier Penya</b> <<a href="mailto:xavier.penya@epfl.ch">
xavier.penya@epfl.ch</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div bgcolor="#ffffff">
<div><font face="Arial" size="2">The former question doesn't
matter because I suppose I can trick the program in order to have a 2D
solution.</font></div>
<div><font face="Arial" size="2">The actual problem is that even in 3D the
result image is all zeros (using the bias coefficients of an image previously
bias-corrected by the ImageBiasCorrector).</font></div>
<div><font face="Arial" size="2">Is it a bug? I beg your help. Thanks a
lot.</font></div><div><span class="e" id="q_1119018a9d81d321_1">
<div><font face="Arial" size="2"></font> </div>
<div style="font-family: arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">----- Original Message -----
<div style="background: rgb(228, 228, 228) none repeat scroll 0% 50%; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;"><b>From:</b> <a title="xavier.penya@epfl.ch" href="mailto:xavier.penya@epfl.ch" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
Xavier Penya</a>
</div>
<div><b>To:</b> <a title="insight-users@itk.org" href="mailto:insight-users@itk.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">insight-users@itk.org</a> </div>
<div><b>Sent:</b> Monday, March 26, 2007 6:13 PM</div>
<div><b>Subject:</b> ImageType::ImageDimension </div></div>
<div><font face="Arial" size="2"></font><br></div>
<div><font face="Arial" size="2">
<div><font face="Arial" size="2">Hello,</font></div>
<div><font face="Arial" size="2">I insisct: I tried everything just to put the
BiasImageGenerator in 2D mode instead of the 3D one, but everything
failed...</font></div>
<div><font face="Arial" size="2">Can somebody tell me where is defined the var
ImageType? It is the root of the problem, due to the part of the
code:</font></div>
<div><font face="Arial"><font size="2"><font face="Arial" size="2"></font></font></font> </div><font size="2">
<blockquote dir="ltr" style="margin-right: 0px;">
<div dir="ltr"></div></blockquote></font><font face="Arial"><font color="#0000ff" size="2">if</font><font size="2">(dimension != </font><font color="#0000ff" size="2">static_cast</font><font size="2"><</font><font color="#0000ff" size="2">
int</font></font><font size="2"><font face="Arial">>(ImageType::ImageDimension))</font></font></font></div>
<div dir="ltr"><font face="Arial">{</font></div>
<blockquote dir="ltr" style="margin-right: 0px;">
<div dir="ltr"><font face="Arial">std::cout << "Currently compiled to only
support "</font></div>
<div dir="ltr"><font face="Arial"><< ImageType::ImageDimension << "
dimensional images."</font></div>
<div dir="ltr"><font face="Arial"><< std::endl;</font></div>
<div dir="ltr"><font face="Arial">exit(0);</font></div></blockquote>
<div dir="ltr"><font face="Arial">}</font></div>
<div dir="ltr"><font face="Arial"><font face="Arial"></font></font> </div>
<div dir="ltr" style="margin-right: 0px;"><font face="Arial">If I put "dimension=2"
it shows the error message because ImageType::ImageDimension is always 3. The
problem is that I cannot change (I even cannot
reach) ImageType::ImageDimension.</font></div>
<div dir="ltr" style="margin-right: 0px;"><font face="Arial">I need your help
please!</font></div>
<div dir="ltr" style="margin-right: 0px;"><font face="Arial"><font face="Arial"></font></font> </div>
<div dir="ltr" style="margin-right: 0px;"><font face="Arial">
Xavier</font></div></span></div></div>
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