<div dir="ltr"><div><div><br></div>I just tried your code on two different dicom datasets, a ct and an mr.<br><br></div>Both worked for me.<br>./DICOMTest ~/Data/itkTestcases/Back\ to\ Front/ .<br>ITK Version: 4.5<br>Stats for file: /home/lorensen/Data/itkTestcases/Back to Front//i24389.MRDC.34<br>
Min: 0, Max: 293, Mean: 28.7654, Sigma: 37.2513, Variance: 1387.66, Sum: 1.88517e+06<br>Stats for file: ./file00.dcm<br>Min: 0, Max: 293, Mean: 28.7654, Sigma: 37.2513, Variance: 1387.66, Sum: 1.88517e+06<br>[build] ./DICOMTest ~/Data/NAV/CT/ ./<br>
ITK Version: 4.5<br>Stats for file: /home/lorensen/Data/NAV/CT//ct.1<br>Min: -1024, Max: 31744, Mean: 6277.24, Sigma: 13249.9, Variance: 1.75559e+08, Sum: 1.64554e+09<br>Stats for file: .//file00.dcm<br>Min: -1024, Max: 31744, Mean: 6277.24, Sigma: 13249.9, Variance: 1.75559e+08, Sum: 1.64554e+09<br>
<br><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Aug 12, 2013 at 11:46 AM, Constantine Zakkaroff <span dir="ltr"><<a href="mailto:mnkz@leeds.ac.uk" target="_blank">mnkz@leeds.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Brad,<br>
<br>
Yes, here's the minimal code:<br>
<br>
******************************<u></u>******************************<u></u>************<br>
#include <cstdlib><br>
#include <itkImage.h><br>
#include <itkMetaImageIO.h><br>
#include <itkGDCMImageIO.h><br>
#include <itkGDCMSeriesFileNames.h><br>
#include <itkImageFileReader.h><br>
#include <itkImageFileWriter.h><br>
#include <itkStatisticsImageFilter.h><br>
<br>
int main(int argc, char *argv[])<br>
{<br>
std::clog << "ITK Version: " << ITK_VERSION_STRING << std::endl;<br>
<br>
typedef itk::GDCMSeriesFileNames NamesGeneratorType;<br>
typedef itk::Image<short, 3> ImageType;<br>
<br>
NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();<br>
namesGenerator-><u></u>SetUseSeriesDetails(true);<br>
namesGenerator-><u></u>SetInputDirectory(argv[1]);<br>
<br>
typedef itk::StatisticsImageFilter<<u></u>ImageType> StatsFilterType;<br>
typedef itk::ImageFileReader<<u></u>ImageType> ImageReaderType;<br>
typedef itk::ImageFileWriter<<u></u>ImageType> ImageWriterType;<br>
<br>
ImageReaderType::Pointer imageReader0 = ImageReaderType::New();<br>
imageReader0->SetImageIO(itk::<u></u>GDCMImageIO::New());<br>
StatsFilterType::Pointer statsFilter0 = StatsFilterType::New();<br>
imageReader0->SetFileName(<u></u>namesGenerator-><u></u>GetInputFileNames()[0]);<br>
statsFilter0->SetInput(<u></u>imageReader0->GetOutput());<br>
statsFilter0->Update();<br>
<br>
std::clog << "Stats for file: " << namesGenerator-><u></u>GetInputFileNames()[0] << std::endl;<br>
std::clog <<<br>
"Min: " << statsFilter0->GetMinimum() << ", "<br>
"Max: " << statsFilter0->GetMaximum() << ", "<br>
"Mean: " << statsFilter0->GetMean() << ", "<br>
"Sigma: " << statsFilter0->GetSigma() << ", "<br>
"Variance: " << statsFilter0->GetVariance() << ", "<br>
"Sum: " << statsFilter0->GetSum()<br>
<< std::endl;<br>
<br>
ImageWriterType::Pointer imageWriter0 = ImageWriterType::New();<br>
imageWriter0->SetInput(<u></u>imageReader0->GetOutput());<br>
imageWriter0->SetImageIO(itk::<u></u>GDCMImageIO::New());<br>
std::string fileName0 = std::string(argv[2]) + "/file00.dcm";<br>
imageWriter0->SetFileName(<u></u>fileName0);<br>
imageWriter0->Update();<br>
<br>
ImageReaderType::Pointer imageReader1 = ImageReaderType::New();<br>
imageReader1->SetImageIO(itk::<u></u>GDCMImageIO::New());<br>
StatsFilterType::Pointer statsFilter1 = StatsFilterType::New();<br>
imageReader1->SetFileName(<u></u>fileName0);<br>
statsFilter1->SetInput(<u></u>imageReader1->GetOutput());<br>
statsFilter1->Update();<br>
<br>
std::clog << "Stats for file: " << fileName0 << std::endl;<br>
std::clog <<<br>
"Min: " << statsFilter1->GetMinimum() << ", "<br>
"Max: " << statsFilter1->GetMaximum() << ", "<br>
"Mean: " << statsFilter1->GetMean() << ", "<br>
"Sigma: " << statsFilter1->GetSigma() << ", "<br>
"Variance: " << statsFilter1->GetVariance() << ", "<br>
"Sum: " << statsFilter1->GetSum()<br>
<< std::endl;<br>
<br>
system("pause");<br>
<br>
return EXIT_SUCCESS;<br>
}<br>
******************************<u></u>******************************<u></u>************<br>
<br>
Many thanks,<br>
Constantine<div class="HOEnZb"><div class="h5"><br>
<br>
On 12/08/2013 14:48, Bradley Lowekamp wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Do you have the code to share so that it can be easily reproduced?<br>
<br>
<br>
Thanks,<br>
Brad<br>
<br>
On Aug 12, 2013, at 9:33 AM, Constantine Zakkaroff <<a href="mailto:mnkz@leeds.ac.uk" target="_blank">mnkz@leeds.ac.uk</a>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello ALL,<br>
<br>
I'm wondering if anyone can explain what's going on with the changing image intensities in a read-write-read round-trip. I think it's a bug, but the <a href="http://issues.itk.org" target="_blank">issues.itk.org</a> is unresponsive at the moment. Another bug? ;)<br>
<br>
Anyhow, the strange thing is that the results for the round trip read-write-read test are very different for ITK 3.20 and ITK 4.4.1.<br>
<br>
I use to StatisticsImageFilter to examine the intensity values. Here's what happens, when I simply read a DICOM image, print stats, save the image and read it again, followed by printing the stats:<br>
<br>
ITK Version: 3.20<br>
Stats for original file:<br>
Min: 0, Max: 2474, Mean: 169.236, Sigma: 256.719, Variance: 65904.7, Sum: 1.40371e+007<br>
Stats for saved file:<br>
Min: 0, Max: 2471, Mean: 167.132, Sigma: 256.125, Variance: 65600.1, Sum: 1.38626e+007<br>
<br>
ITK Version: 4.4<br>
Stats for original file:<br>
Min: 0, Max: 2474, Mean: 169.236, Sigma: 256.719, Variance: 65904.7, Sum: 1.40371e+007<br>
Stats for saved file:<br>
Min: 0, Max: 7446, Mean: 509.114, Sigma: 772.59, Variance: 596895, Sum: 4.22279e+007<br>
<br>
In both cases the code is identical. Just compiled against different versions of ITK. The images are read and written as itk::Image<unsigned short, 3>, with no processing, no changes to any aspect of the images.<br>
<br>
So, ITK 3.20 introduces a small change, which I'm pretty sure shouldn't be there. But in ITK 4.4.1 the scale of intensities changes three-fold.<br>
<br>
I'd not be surprised by a change of this magnitude if I was photocopying those images, but not when using digital software and hardware. :^) Is there something I'm not understanding here?<br>
<br>
None of this happens with read(DICOM)-write(MHD)-read(<u></u>MHD), where the original and round-trip values are identical:<br>
Stats for saved file: file0.mhd<br>
Min: 0, Max: 2474, Mean: 169.236, Sigma: 256.719, Variance: 65904.7, Sum: 1.40371e+007<br>
<br>
Many thanks,<br>
Constantine<br>
<br>
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