<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">'x' is just a symbol for the different levels<div>(not multiplication).<br><div><br></div><div>50x100x20 = 50 iterations at the first level, </div><div>100 iterations at the second level, and 20</div><div>iterations at the third level. </div><div><br></div><div>At this point I don't know that I can provide</div><div>any more help. I don't have access to Visual</div><div>C++ 2008 express and all the windows </div><div>builds of the itkN4... class work just fine. </div><div>Your command line call, other than the 'x',</div><div>problem looks fine. It should work.</div><div><br></div><div>Nick</div><div><br></div><div><br></div><div><br><div><div>On Jan 10, 2012, at 5:09 AM, Wenwu wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Nick,<br><br>sorry for my misunderstanding of the symbol meaning.<br><br><br><br><div class="gmail_quote">On Tue, Jan 10, 2012 at 12:58 PM, Nicholas Tustison <span dir="ltr"><<a href="mailto:ntustison@gmail.com">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">Why are you using this <div><br></div><div>-c [50*50*50, 0.001]</div><div><br></div>
<div>
for the convergence? It should be</div><div><br></div><div>-c [50x50x50, 0.001]</div></div></blockquote><div>I want to know what is the mean of the `x`? <br><br>I correct it as char `x` and Multiply symbol, the result is the same!<br>
<br><br> </div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word"><div><br></div><div><br></div><div><br><div><div class="im">
<div>On Jan 10, 2012, at 3:11 AM, Wenwu wrote:</div><br></div><blockquote type="cite"><div class="im">Hi Nick,<br><br>Today, I run the N4 in Visual c++2008 express, and the result is incredible! The source data I used is t8slice.nii.gz contained by N4! The arguments are:<br>
<br>-d 2 -i e:\t81slice.nii.gz -o e:\t81sliceCorrect.mhd -x e:\t81mask.nii.gz -s 2 -c [50*50*50, 0.001] -b [100, 3] -t [0.15, 0.001, 200]<br>
<br>The corrected image is amazing:<br><br></div><div><div class="h5"><span><t81sliceCorrect.png></span> <br><br><br>It should be a fully wrong result! Could you help me point out where I made the mistake? <br>
<br><br>Thank you very much!!<br><br><br>Wenwu<br><br><br><br><div class="gmail_quote">On Mon, Jan 9, 2012 at 10:51 PM, Wenwu <span dir="ltr"><<a href="mailto:cool.wenwu@gmail.com" target="_blank">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 Nick,<br><br><div class="gmail_quote"><div>On Mon, Jan 9, 2012 at 7:12 PM, Nicholas Tustison <span dir="ltr"><<a href="mailto:ntustison@gmail.com" target="_blank">ntustison@gmail.com</a>></span> wrote:<br>
</div><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>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" target="_blank">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></div></blockquote><div>I am waiting for your good news! I am not sure if I made a mistake in Dicom writing part!</div><div><div>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word"><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></blockquote><div><br></div></div><div>Sorry, I made a mistake here, however it was right in the program.</div><div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word"><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></blockquote></div><div>Ok, No pb. </div><div><div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word"><div></div><div><br><div><div><div>On Jan 9, 2012, at 10:18 AM, Wenwu wrote:</div><br></div><blockquote type="cite"><div>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><div class="gmail_quote"><div>
On Mon, Jan 9, 2012 at 6:13 PM, Wenwu <span dir="ltr"><<a href="mailto:cool.wenwu@gmail.com" target="_blank">cool.wenwu@gmail.com</a>></span> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
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></div><div><div><span><image22_BC.png></span><div><div>
<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><div>-- <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></div></div></blockquote></div><div><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>
</div></div></blockquote></div><br></div></div></blockquote></div></div></div><div><div><br><br clear="all"><div><br></div>-- <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>
</div></div></blockquote></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>
</blockquote></div><br></div></div></body></html>