[Insight-users] Some questions in understanding the N4ITK

[Nicholas Tustison]

Hi Wenwu,

First, I would donwload and updated version of N4.cxx

http://advants.svn.sourceforge.net/viewvc/advants/Examples/N4BiasFieldCorrection.cxx?view=log

as I don't use N4.cxx anymore and have updated.

Second, your command line convergence parameter 
is incorrect.  I'm guessing you meant

-c [20x20x20,0.001]

Doing that works for me.

Nick

Ps. I'm cc'ing the insight users list.  I'd recommend keeping this 
conversation on the list---I know it's useful for me to search the
archives of previous conversations to find solutions to my
problems.


On Jan 9, 2012, at 10:18 AM, Wenwu wrote:

> Sorry, I forgot to show the commander to run this test. The code is as following:
> 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] 
> 
> 
> On Mon, Jan 9, 2012 at 6:13 PM, Wenwu <cool.wenwu at gmail.com> wrote:
> Hi Nicholas,
> 
> Thank you very much for your kind help! Now there is another problem needed your help!
> 
> 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? 
> 
> In addition, after adding code of  writing Dicom format, there is an debug error. The code can run in my other program.
> The code was added as this:
> 
> if (outputOption->GetNumberOfParameters() ==0 )
> {
> ...
> typedef itk::GDCMImageIO ImageIOType;
> ImageIOType::Pointer gdcImageTypeIO = ImageIOType::New();
> ...
> Writer->SetFileName(gdcImageTypeIO);
> }
> // of course, other two cases, I also add them
> 
> Could you please give some prompt about it?
> 
> The original MRI image is attached.
> The result of the N4 processing with .mhd Format is as following:
> 
> <image22_BC.png>
> 
> 
> 
> 
> 
> 
>  
> 
> On Mon, Jan 9, 2012 at 5:17 PM, Nicholas Tustison <ntustison at gmail.com> wrote:
> Hi Wenwu,
> 
>> 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:
>>  
>> itk_add_test(NAME itkN4BiasFieldCorrectionImageFilterTest1
>>       COMMAND ITKBiasCorrectionTestDriver
>>       --compare DATA{Baseline/N4ControlPoints_3D.nii.gz}
>>                ${ITK_TEST_OUTPUT_DIR}/N4ControlPoints_3D.nii.gz
>>     itkN4BiasFieldCorrectionImageFilterTest
>>     2
>>     DATA{${ITK_DATA_ROOT}/Input/HeadMRVolumeCompressed.mha}            # input
>>     ${ITK_TEST_OUTPUT_DIR}//N4ControlPoints_3D.nii.gz                  # control point lattice  . , I also can not understand the mean of this parameter
>> 
>>     3                                                                       # shrink factor
>>     10x10x10                                                           # number of iterations
>>     none                                                               # mask
>>     150                                                                # spline distance
>>     )
>> 
> 
> The control point lattice is the output defining the bias field.  
> You need to remember that this is a test, not a user-level
> application which is what N4.cxx encapsulates.
> 
> Nick
> 
> 
> 
> 
> -- 
> Wenwu Zhu
> IRCAD
> University of Strasbourg, France
> Email address: cool.wenwu at gmail.com
> 
> 
> 
> 
> -- 
> Wenwu Zhu
> IRCAD
> University of Strasbourg, France
> Email address: cool.wenwu at gmail.com
> 

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