<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Wenwu,<div><br></div><div>First, I would donwload and updated version of N4.cxx</div><div><br></div><div><a href="http://advants.svn.sourceforge.net/viewvc/advants/Examples/N4BiasFieldCorrection.cxx?view=log">http://advants.svn.sourceforge.net/viewvc/advants/Examples/N4BiasFieldCorrection.cxx?view=log</a></div><div><br></div><div>as I don't use N4.cxx anymore and have updated.</div><div><br></div><div>Second, your command line convergence parameter </div><div>is incorrect. I'm guessing you meant</div><div><br></div><div>-c [20x20x20,0.001]</div><div><br></div><div>Doing that works for me.</div><div><br></div><div>Nick</div><div><br></div><div>Ps. I'm cc'ing the insight users list. I'd recommend keeping this </div><div>conversation on the list---I know it's useful for me to search the</div><div>archives of previous conversations to find solutions to my</div><div>problems.</div><div><br></div><div><br><div><div>On Jan 9, 2012, at 10:18 AM, Wenwu wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Sorry, I forgot to show the commander to run this test. The code is as following:<br>N4.exe -d 2 -i e:/image_22 -o e:/image_22BC.mhd -s 2 -c [20*20*20m 0.001] -b [200,3] -t [0.15 0.001, 200] <br><br><br><div class="gmail_quote">
On Mon, Jan 9, 2012 at 6:13 PM, Wenwu <span dir="ltr"><<a href="mailto:cool.wenwu@gmail.com">cool.wenwu@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Nicholas,<br><br>Thank you very much for your kind help! Now there is another problem needed your help!<br><br>I run N4 with Dicom image(Reading code I added) to test, because the N4 seems can not output Dicom format, so I choose to output .mhd file. However the outcome is very bad. Could you please give me some suggestion? <br>
<br>In addition, after adding code of writing Dicom format, there is an debug error. The code can run in my other program.<br>The code was added as this:<br><br>if (outputOption->GetNumberOfParameters() ==0 )<br>{<br>
...<br>typedef itk::GDCMImageIO ImageIOType;<br>ImageIOType::Pointer gdcImageTypeIO = ImageIOType::New();<br>...<br>Writer->SetFileName(gdcImageTypeIO);<br>}<br>// of course, other two cases, I also add them<br><br>Could you please give some prompt about it?<br>
<br>The original MRI image is attached.<br>The result of the N4 processing with .mhd Format is as following:<br><br><span><image22_BC.png></span><div class="HOEnZb"><div class="h5">
<br><br><br><br><br><br> <br>
<br><div class="gmail_quote">On Mon, Jan 9, 2012 at 5:17 PM, Nicholas Tustison <span dir="ltr"><<a href="mailto:ntustison@gmail.com" target="_blank">ntustison@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Wenwu,<div><br></div><div><div><div><blockquote type="cite">There are some problems when I learn the N4ITK. Firstly, in the paper-"N4ITK:Nick's N3 ITK Implementation For MRI Bias Field Correction" , I found there are 9 parameters (m_MaskMabel, m_numberOfHistogamBins, m_WeinerFilterNoise, m_BiasFieldFullWitdthAtHalfMaximum... ,)need to set, it can also be found in the N4ITK package. However, in the lastest ITK4.0, in the project-ITKBiasCorrectionTestDriver, I open the CMakeLists.txt, and some code is as followiing:<br>
<br>itk_add_test(NAME itkN4BiasFieldCorrectionImageFilterTest1<br> COMMAND ITKBiasCorrectionTestDriver<br> --compare DATA{Baseline/N4ControlPoints_3D.nii.gz}<br> ${ITK_TEST_OUTPUT_DIR}/N4ControlPoints_3D.nii.gz<br>
itkN4BiasFieldCorrectionImageFilterTest<br> 2<br> DATA{${ITK_DATA_ROOT}/Input/HeadMRVolumeCompressed.mha} # input<br> ${ITK_TEST_OUTPUT_DIR}//N4ControlPoints_3D.nii.gz # <b>control point lattice .</b> , I also can not understand the mean of this parameter<br>
<br> 3 # shrink factor<br> 10x10x10 # number of iterations<br> none # mask<br>
150 # spline distance<br> )<br><br></blockquote><div><br></div></div><div>The control point lattice is the output defining the bias field. </div><div>
You need to remember that this is a test, not a user-level</div><div>application which is what N4.cxx encapsulates.</div><div><br></div><div>Nick</div><div><br></div></div></div></div></blockquote></div><br><br clear="all">
<br></div></div><div class="HOEnZb"><div class="h5">-- <br><div>Wenwu Zhu</div>
<div>IRCAD<br>University of Strasbourg, France<br>Email address: <a href="mailto:cool.wenwu@gmail.com" target="_blank">cool.wenwu@gmail.com</a></div><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br><div>Wenwu Zhu</div>
<div>IRCAD<br>University of Strasbourg, France<br>Email address: <a href="mailto:cool.wenwu@gmail.com" target="_blank">cool.wenwu@gmail.com</a></div><br>
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