From juandelcruce1 at gmail.com  Wed Jul  4 11:56:03 2018
From: juandelcruce1 at gmail.com (C Juan)
Date: Wed, 4 Jul 2018 17:56:03 +0200
Subject: [ITK-users] sitk.ReadImage for known deformation fields in dcm or
 niftii
Message-ID: <CAFtg9AKUoK0BbJiuSRr5Di9K1TVxE01ExAj+f6v+Dt6ybCLDgw@mail.gmail.com>

Hi all,

I am new user of  SimpleITK and for a project I want to read a known
deformation field, previously calculated from another software, which is
stored in dcm format, (could be also in Nifti format).

When I use:

dis = sitk.ReadImage('dvf.dcm', sitk.sitkVectorFloat64)


Throws the error:

RuntimeError: Exception thrown in SimpleITK ReadImage:
C:\d\VS14-Win64-pkg\SimpleITK\Code\IO\src\sitkImageFileReader.cxx:248:
sitk::ERROR: The file has unsupported 5 dimensions.

I am not really sure if simply using ReadImage is the right approach. I
would really appreciate if you can give me some ideas how to solve this
issue.

Thanks!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://itk.org/pipermail/insight-users/attachments/20180704/ce920810/attachment.html>

From lasso at queensu.ca  Wed Jul  4 12:38:17 2018
From: lasso at queensu.ca (Andras Lasso)
Date: Wed, 4 Jul 2018 16:38:17 +0000
Subject: [ITK-users] [ITK] sitk.ReadImage for known deformation fields
 in dcm or niftii
In-Reply-To: <CAFtg9AKUoK0BbJiuSRr5Di9K1TVxE01ExAj+f6v+Dt6ybCLDgw@mail.gmail.com>
References: <CAFtg9AKUoK0BbJiuSRr5Di9K1TVxE01ExAj+f6v+Dt6ybCLDgw@mail.gmail.com>
Message-ID: <YQBPR0101MB185980DD09A28C0C3925B1ADD8410@YQBPR0101MB1859.CANPRD01.PROD.OUTLOOK.COM>

I think 3D Slicer can import registration objects from DICOM. You can either save the displacement field to file or use SimpleITK in 3D Slicer. To further discuss this, please post on ITK forum (https://discourse.itk.org/).

Andras

From: Community <community-bounces at itk.org> On Behalf Of C Juan
Sent: Wednesday, July 4, 2018 11:56 AM
To: insight-users at itk.org
Subject: [ITK] [ITK-users] sitk.ReadImage for known deformation fields in dcm or niftii

Hi all,

I am new user of  SimpleITK and for a project I want to read a known deformation field, previously calculated from another software, which is stored in dcm format, (could be also in Nifti format).

When I use:


dis = sitk.ReadImage('dvf.dcm', sitk.sitkVectorFloat64)

Throws the error:

RuntimeError: Exception thrown in SimpleITK ReadImage: C:\d\VS14-Win64-pkg\SimpleITK\Code\IO\src\sitkImageFileReader.cxx:248:
sitk::ERROR: The file has unsupported 5 dimensions.

I am not really sure if simply using ReadImage is the right approach. I would really appreciate if you can give me some ideas how to solve this issue.

Thanks!

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://itk.org/pipermail/insight-users/attachments/20180704/667245ee/attachment.html>

From ashahrior.91994 at gmail.com  Thu Jul  5 09:52:02 2018
From: ashahrior.91994 at gmail.com (Ashef Shahrior)
Date: Thu, 5 Jul 2018 19:52:02 +0600
Subject: [ITK-users] ITK and VTK connection problem
Message-ID: <CAB8nWDw+sb+mv76GaV9EtqOHuptjHFM6kSyZ=Qq92DO5yL615Q@mail.gmail.com>

>From ITK Software Guide Book, I am trying to do Region Growing - Connected
Threshold segmentation and show it using VTK. In the guide book, the
segmented image is written into another file. But I don't want to write it
but rather display it using VTK renderer. But it seems to be not working.
Can anyone see my code and help me out, please? Here's my code:

#include <iostream>
#include <string.h>
#include <windows.h>
#include <time.h>
#include <dos.h>

#include "itkConnectedThresholdImageFilter.h"

#include "itkImage.h"
#include "itkCastImageFilter.h"

#include "itkCurvatureFlowImageFilter.h"

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

#include "itkVTKImageExport.h"
#include "itkVTKImageImport.h"
#include "itkRGBPixel.h"

#include "vtkImageData.h"
#include "vtkImageImport.h"
#include "vtkImageExport.h"
#include "vtkImageActor.h"
#include "vtkRenderer.h"
#include "vtkRenderWindow.h"
#include "vtkRenderWindowInteractor.h"
#include "vtkInteractorStyleImage.h"

using namespace std;

template <typename ITK_Exporter, typename VTK_Importer> void
ConnectPipelines(ITK_Exporter exporter, VTK_Importer* importer)
{

importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());

importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
    importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
    importer->SetSpacingCallback(exporter->GetSpacingCallback());
    importer->SetOriginCallback(exporter->GetOriginCallback());
    importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());

importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());

importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
    importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
    importer->SetDataExtentCallback(exporter->GetDataExtentCallback());

importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
    importer->SetCallbackUserData(exporter->GetCallbackUserData());
}

template <typename VTK_Exporter, typename ITK_Importer> void
ConnectPipelines(VTK_Exporter* exporter, ITK_Importer importer)
{

importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());

importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
    importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
    importer->SetSpacingCallback(exporter->GetSpacingCallback());
    importer->SetOriginCallback(exporter->GetOriginCallback());
    importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());

importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());

importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
    importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
    importer->SetDataExtentCallback(exporter->GetDataExtentCallback());

importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
    importer->SetCallbackUserData(exporter->GetCallbackUserData());
}


void main()
{
    char inputImage[1000], seedx[10], seedy[10], lThreshold[100],
uThreshold[100];

    cout<< "Input values: "<<endl;
    cin >> inputImage;
    cin>>seedx;
    cin>>seedy;
    cin>>lThreshold;
    cin>>uThreshold;

    const     unsigned int    Dimension = 2;

    typedef   float           InternalPixelType;
    typedef itk::Image< InternalPixelType, Dimension >  InternalImageType;

    typedef unsigned char                            OutputPixelType;
    typedef itk::Image< OutputPixelType, Dimension > OutputImageType;

    typedef itk::CurvatureFlowImageFilter< InternalImageType,
InternalImageType > CurvatureFlowImageFilterType;

    CurvatureFlowImageFilterType::Pointer smoothing =
CurvatureFlowImageFilterType::New();

    typedef itk::ConnectedThresholdImageFilter< InternalImageType,
InternalImageType > ConnectedFilterType;

    ConnectedFilterType::Pointer connectedThreshold =
ConnectedFilterType::New();

    typedef itk::CastImageFilter< InternalImageType, OutputImageType >
CastingFilterType;

    CastingFilterType::Pointer caster = CastingFilterType::New();

    typedef  itk::ImageFileReader< InternalImageType > ReaderType;
    typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;

    ReaderType::Pointer reader = ReaderType::New();
    WriterType::Pointer writer = WriterType::New();

    reader->SetFileName( inputImage );
    reader->Update();
    //writer->SetFileName( outputImage );

    smoothing->SetInput( reader->GetOutput() );
    smoothing->SetNumberOfIterations( 5 );
    smoothing->SetTimeStep( 0.125 );

    //writer->SetInput( caster->GetOutput() );
    const InternalPixelType lowerThreshold = atof( lThreshold );
    const InternalPixelType upperThreshold = atof( uThreshold );

    connectedThreshold->SetInput( smoothing->GetOutput() );
    connectedThreshold->SetLower(  lowerThreshold  );
    connectedThreshold->SetUpper(  upperThreshold  );

    connectedThreshold->SetReplaceValue( 255 );

    InternalImageType::IndexType  index;

    index[0] = atoi( seedx );
    index[1] = atoi( seedy );

    connectedThreshold->SetSeed( index );
    connectedThreshold->Update();

    //caster->SetInput( connectedThreshold->GetOutput() );
caster->SetInput(connectedThreshold->GetOutput());

    typedef itk::VTKImageExport< InternalImageType > ExportFilterType; //
    ExportFilterType::Pointer itkExporter = ExportFilterType::New(); //

        //itkExporter->SetInput( caster->GetOutput() ); // this line gives
me error warning, so i did the following line
itkExporter->SetInput(connectedThreshold->GetOutput());



    vtkImageImport* vtkImporter = vtkImageImport::New();  //
    ConnectPipelines(itkExporter, vtkImporter);

    typedef itk::VTKImageImport< InternalImageType > ImportFilterType; //
    ImportFilterType::Pointer itkImporter = ImportFilterType::New(); //


    vtkImageExport* vtkExporter = vtkImageExport::New();
    ConnectPipelines(vtkExporter, itkImporter);

#if VTK_MAJOR_VERSION <= 5
    vtkExporter->SetInput( vtkImporter->GetOutput() );
#else
    vtkImporter->Update();
    vtkExporter->SetInputData( vtkImporter->GetOutput() );
#endif

    vtkImageActor* actor = vtkImageActor::New();
#if VTK_MAJOR_VERSION <= 5
    actor->SetInput(vtkImporter->GetOutput());
#else
    actor->SetInputData(vtkImporter->GetOutput());
#endif

    vtkInteractorStyleImage * interactorStyle =
vtkInteractorStyleImage::New();

    vtkRenderer* renderer = vtkRenderer::New();
    vtkRenderWindow* renWin = vtkRenderWindow::New();
    vtkRenderWindowInteractor* iren = vtkRenderWindowInteractor::New();

    renWin->SetSize(500, 500);
    renWin->AddRenderer(renderer);
    iren->SetRenderWindow(renWin);
    iren->SetInteractorStyle( interactorStyle );

    renderer->AddActor(actor);
    renderer->SetBackground(0.4392, 0.5020, 0.5647);

    renWin->Render();
    iren->Start();

    actor->Delete();
    interactorStyle->Delete();
    vtkImporter->Delete();
    vtkExporter->Delete();
    renWin->Delete();
    renderer->Delete();
    iren->Delete();
}

Thanks in advance.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://itk.org/pipermail/insight-users/attachments/20180705/095b913b/attachment.html>

From matt.mccormick at kitware.com  Thu Jul  5 11:56:31 2018
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 5 Jul 2018 11:56:31 -0400
Subject: [ITK-users] ITK and VTK connection problem
In-Reply-To: <CAB8nWDw+sb+mv76GaV9EtqOHuptjHFM6kSyZ=Qq92DO5yL615Q@mail.gmail.com>
References: <CAB8nWDw+sb+mv76GaV9EtqOHuptjHFM6kSyZ=Qq92DO5yL615Q@mail.gmail.com>
Message-ID: <CALzTN-SxwC0aFpATd5Wt_090QBS2A-YphFKV3UfZZsDOmsP8kA@mail.gmail.com>

Hi,

The itk::ImageToVTKImageFilter should be used instead of the
itk::VTKImageImport class directly. See, for example:

  https://itk.org/ITKExamples/src/Bridge/VtkGlue/ConvertAnitkImageTovtkImageData/Documentation.html

HTH,
Matt
On Thu, Jul 5, 2018 at 9:52 AM Ashef Shahrior <ashahrior.91994 at gmail.com> wrote:
>
> From ITK Software Guide Book, I am trying to do Region Growing - Connected Threshold segmentation and show it using VTK. In the guide book, the segmented image is written into another file. But I don't want to write it but rather display it using VTK renderer. But it seems to be not working. Can anyone see my code and help me out, please? Here's my code:
>
> #include <iostream>
> #include <string.h>
> #include <windows.h>
> #include <time.h>
> #include <dos.h>
>
> #include "itkConnectedThresholdImageFilter.h"
>
> #include "itkImage.h"
> #include "itkCastImageFilter.h"
>
> #include "itkCurvatureFlowImageFilter.h"
>
> #include "itkImageFileReader.h"
> #include "itkImageFileWriter.h"
>
> #include "itkVTKImageExport.h"
> #include "itkVTKImageImport.h"
> #include "itkRGBPixel.h"
>
> #include "vtkImageData.h"
> #include "vtkImageImport.h"
> #include "vtkImageExport.h"
> #include "vtkImageActor.h"
> #include "vtkRenderer.h"
> #include "vtkRenderWindow.h"
> #include "vtkRenderWindowInteractor.h"
> #include "vtkInteractorStyleImage.h"
>
> using namespace std;
>
> template <typename ITK_Exporter, typename VTK_Importer> void ConnectPipelines(ITK_Exporter exporter, VTK_Importer* importer)
> {
>     importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());
>     importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
>     importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
>     importer->SetSpacingCallback(exporter->GetSpacingCallback());
>     importer->SetOriginCallback(exporter->GetOriginCallback());
>     importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
>     importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());
>     importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
>     importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
>     importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
>     importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
>     importer->SetCallbackUserData(exporter->GetCallbackUserData());
> }
>
> template <typename VTK_Exporter, typename ITK_Importer> void ConnectPipelines(VTK_Exporter* exporter, ITK_Importer importer)
> {
>     importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());
>     importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
>     importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
>     importer->SetSpacingCallback(exporter->GetSpacingCallback());
>     importer->SetOriginCallback(exporter->GetOriginCallback());
>     importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
>     importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());
>     importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
>     importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
>     importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
>     importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
>     importer->SetCallbackUserData(exporter->GetCallbackUserData());
> }
>
>
> void main()
> {
>     char inputImage[1000], seedx[10], seedy[10], lThreshold[100], uThreshold[100];
>
>     cout<< "Input values: "<<endl;
>     cin >> inputImage;
>     cin>>seedx;
>     cin>>seedy;
>     cin>>lThreshold;
>     cin>>uThreshold;
>
>     const     unsigned int    Dimension = 2;
>
>     typedef   float           InternalPixelType;
>     typedef itk::Image< InternalPixelType, Dimension >  InternalImageType;
>
>     typedef unsigned char                            OutputPixelType;
>     typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>
>     typedef itk::CurvatureFlowImageFilter< InternalImageType, InternalImageType > CurvatureFlowImageFilterType;
>
>     CurvatureFlowImageFilterType::Pointer smoothing = CurvatureFlowImageFilterType::New();
>
>     typedef itk::ConnectedThresholdImageFilter< InternalImageType, InternalImageType > ConnectedFilterType;
>
>     ConnectedFilterType::Pointer connectedThreshold = ConnectedFilterType::New();
>
>     typedef itk::CastImageFilter< InternalImageType, OutputImageType > CastingFilterType;
>
>     CastingFilterType::Pointer caster = CastingFilterType::New();
>
>     typedef  itk::ImageFileReader< InternalImageType > ReaderType;
>     typedef  itk::ImageFileWriter<  OutputImageType  > WriterType;
>
>     ReaderType::Pointer reader = ReaderType::New();
>     WriterType::Pointer writer = WriterType::New();
>
>     reader->SetFileName( inputImage );
>     reader->Update();
>     //writer->SetFileName( outputImage );
>
>     smoothing->SetInput( reader->GetOutput() );
>     smoothing->SetNumberOfIterations( 5 );
>     smoothing->SetTimeStep( 0.125 );
>
>     //writer->SetInput( caster->GetOutput() );
>     const InternalPixelType lowerThreshold = atof( lThreshold );
>     const InternalPixelType upperThreshold = atof( uThreshold );
>
>     connectedThreshold->SetInput( smoothing->GetOutput() );
>     connectedThreshold->SetLower(  lowerThreshold  );
>     connectedThreshold->SetUpper(  upperThreshold  );
>
>     connectedThreshold->SetReplaceValue( 255 );
>
>     InternalImageType::IndexType  index;
>
>     index[0] = atoi( seedx );
>     index[1] = atoi( seedy );
>
>     connectedThreshold->SetSeed( index );
>     connectedThreshold->Update();
>
>     //caster->SetInput( connectedThreshold->GetOutput() );
> caster->SetInput(connectedThreshold->GetOutput());
>
>     typedef itk::VTKImageExport< InternalImageType > ExportFilterType; //
>     ExportFilterType::Pointer itkExporter = ExportFilterType::New(); //
>
>         //itkExporter->SetInput( caster->GetOutput() ); // this line gives me error warning, so i did the following line
> itkExporter->SetInput(connectedThreshold->GetOutput());
>
>
>
>     vtkImageImport* vtkImporter = vtkImageImport::New();  //
>     ConnectPipelines(itkExporter, vtkImporter);
>
>     typedef itk::VTKImageImport< InternalImageType > ImportFilterType; //
>     ImportFilterType::Pointer itkImporter = ImportFilterType::New(); //
>
>
>     vtkImageExport* vtkExporter = vtkImageExport::New();
>     ConnectPipelines(vtkExporter, itkImporter);
>
> #if VTK_MAJOR_VERSION <= 5
>     vtkExporter->SetInput( vtkImporter->GetOutput() );
> #else
>     vtkImporter->Update();
>     vtkExporter->SetInputData( vtkImporter->GetOutput() );
> #endif
>
>     vtkImageActor* actor = vtkImageActor::New();
> #if VTK_MAJOR_VERSION <= 5
>     actor->SetInput(vtkImporter->GetOutput());
> #else
>     actor->SetInputData(vtkImporter->GetOutput());
> #endif
>
>     vtkInteractorStyleImage * interactorStyle = vtkInteractorStyleImage::New();
>
>     vtkRenderer* renderer = vtkRenderer::New();
>     vtkRenderWindow* renWin = vtkRenderWindow::New();
>     vtkRenderWindowInteractor* iren = vtkRenderWindowInteractor::New();
>
>     renWin->SetSize(500, 500);
>     renWin->AddRenderer(renderer);
>     iren->SetRenderWindow(renWin);
>     iren->SetInteractorStyle( interactorStyle );
>
>     renderer->AddActor(actor);
>     renderer->SetBackground(0.4392, 0.5020, 0.5647);
>
>     renWin->Render();
>     iren->Start();
>
>     actor->Delete();
>     interactorStyle->Delete();
>     vtkImporter->Delete();
>     vtkExporter->Delete();
>     renWin->Delete();
>     renderer->Delete();
>     iren->Delete();
> }
>
> Thanks in advance.
> The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> https://itk.org/mailman/listinfo/insight-users

From enslay at gmail.com  Fri Jul  6 20:18:01 2018
From: enslay at gmail.com (Nathan Lay)
Date: Fri, 6 Jul 2018 20:18:01 -0400
Subject: [ITK-users] ITK is more general than medical imaging!
Message-ID: <CAGQZ7vuboDBMoThPCAKkn1+cueBNTh4237aSiVfPY6atC2tHLA@mail.gmail.com>

Just personal observation... but I've been using ITK in a very similar
fashion to medical imaging to do some cartography/geography related work
(my spacing is m instead of mm). And saving extra/custom meta data like
GeoTIFF is something the medical imaging community has been doing for
decades with a plethora of formats (like MetaIO and DICOM). I can also
imagine streaming IO being useful for streaming large sections of the earth
too! It's also really useful to save 16 bit pixels sometimes... and
visualize them (and overlay them on other images or masks).

Why is ITK only a medical imaging toolkit again? A big reason I use ITK for
such *unrelated* work is that its itk::Image carries transformations
around. And that information (and more!) get saved to file too.

I mean doing similar work with PNG/JPG and OpenCV is a nightmare by
comparison when you need to work with lots of different coordinate systems
simultaneously.

Best regards,
Nathan Lay
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://itk.org/pipermail/insight-users/attachments/20180706/9487c83b/attachment.html>

From dzenanz at gmail.com  Sat Jul  7 19:36:00 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Sat, 7 Jul 2018 19:36:00 -0400
Subject: [ITK-users] ITK is more general than medical imaging!
In-Reply-To: <CAGQZ7vuboDBMoThPCAKkn1+cueBNTh4237aSiVfPY6atC2tHLA@mail.gmail.com>
References: <CAGQZ7vuboDBMoThPCAKkn1+cueBNTh4237aSiVfPY6atC2tHLA@mail.gmail.com>
Message-ID: <CAPf2UMTiX87CAaVON+Gw_vbEcMVrmMmbnyGmX_D-kzaQP+e24g@mail.gmail.com>

Hi Nathan,

ITK is NOT only a medical imaging toolkit. It has many other uses. You are
right that it has primarily medical focus, and that is because it has been
primarily funded by NIH.

Thanks for positive feedback. Also, you might want to join the new forum
<https://discourse.itk.org/>.

Regards,
D?enan

On Fri, Jul 6, 2018 at 8:18 PM Nathan Lay <enslay at gmail.com> wrote:

> Just personal observation... but I've been using ITK in a very similar
> fashion to medical imaging to do some cartography/geography related work
> (my spacing is m instead of mm). And saving extra/custom meta data like
> GeoTIFF is something the medical imaging community has been doing for
> decades with a plethora of formats (like MetaIO and DICOM). I can also
> imagine streaming IO being useful for streaming large sections of the earth
> too! It's also really useful to save 16 bit pixels sometimes... and
> visualize them (and overlay them on other images or masks).
>
> Why is ITK only a medical imaging toolkit again? A big reason I use ITK
> for such *unrelated* work is that its itk::Image carries transformations
> around. And that information (and more!) get saved to file too.
>
> I mean doing similar work with PNG/JPG and OpenCV is a nightmare by
> comparison when you need to work with lots of different coordinate systems
> simultaneously.
>
> Best regards,
> Nathan Lay
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> https://itk.org/mailman/listinfo/insight-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://itk.org/pipermail/insight-users/attachments/20180707/0a502b0e/attachment.html>

From matt.mccormick at kitware.com  Mon Jul  9 10:55:17 2018
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 9 Jul 2018 10:55:17 -0400
Subject: [ITK-users] ITK is more general than medical imaging!
In-Reply-To: <CAPf2UMTiX87CAaVON+Gw_vbEcMVrmMmbnyGmX_D-kzaQP+e24g@mail.gmail.com>
References: <CAGQZ7vuboDBMoThPCAKkn1+cueBNTh4237aSiVfPY6atC2tHLA@mail.gmail.com>
 <CAPf2UMTiX87CAaVON+Gw_vbEcMVrmMmbnyGmX_D-kzaQP+e24g@mail.gmail.com>
Message-ID: <CALzTN-RTuvBP8015_b4mW8VzVZYKTQk-WrQyUX6H1eHy-F_1dg@mail.gmail.com>

Hi Nathan,

Yes, ITK's capability for spatial analysis and its general
functionality has a lot to offer many domains. We need your help to
spread the word :-).

Regarding satellite imagery, the ITK-based OrfeoToolbox (OTB) has a
lot to offer also:

  https://www.orfeo-toolbox.org/

Cheers,
Matt
On Sat, Jul 7, 2018 at 7:36 PM D?enan Zuki? <dzenanz at gmail.com> wrote:
>
> Hi Nathan,
>
> ITK is NOT only a medical imaging toolkit. It has many other uses. You are right that it has primarily medical focus, and that is because it has been primarily funded by NIH.
>
> Thanks for positive feedback. Also, you might want to join the new forum.
>
> Regards,
> D?enan
>
> On Fri, Jul 6, 2018 at 8:18 PM Nathan Lay <enslay at gmail.com> wrote:
>>
>> Just personal observation... but I've been using ITK in a very similar fashion to medical imaging to do some cartography/geography related work (my spacing is m instead of mm). And saving extra/custom meta data like GeoTIFF is something the medical imaging community has been doing for decades with a plethora of formats (like MetaIO and DICOM). I can also imagine streaming IO being useful for streaming large sections of the earth too! It's also really useful to save 16 bit pixels sometimes... and visualize them (and overlay them on other images or masks).
>>
>> Why is ITK only a medical imaging toolkit again? A big reason I use ITK for such *unrelated* work is that its itk::Image carries transformations around. And that information (and more!) get saved to file too.
>>
>> I mean doing similar work with PNG/JPG and OpenCV is a nightmare by comparison when you need to work with lots of different coordinate systems simultaneously.
>>
>> Best regards,
>> Nathan Lay
>> The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
>> ________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> https://itk.org/mailman/listinfo/insight-users
>
> The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> https://itk.org/mailman/listinfo/insight-users

From Darren.Thompson at csiro.au  Thu Jul 12 07:36:06 2018
From: Darren.Thompson at csiro.au (Darren.Thompson at csiro.au)
Date: Thu, 12 Jul 2018 11:36:06 +0000
Subject: [ITK-users] ITKModuleTemplate and external modules for use with
 python
Message-ID: <45eec90025e2442c85429ef978da1ecd@exch3-mel.nexus.csiro.au>

Hi All,

I'm revisiting making my own external ITK module (for use in Python) after an initial attempt a while back. This time I've managed to get much further and have managed to successfully create python wheels following the directions on https://github.com/InsightSoftwareConsortium/ITKPythonPackage/blob/master/docs/Build_ITK_Module_Python_packages.rst  , I've created Windows wheels via AppVeyor and linux wheels with CircleCI in addition to locally built versions via the docker based method. All tests are passed successfully.

However, after installing them with pip in a fresh virtual environment in a Python 3.6 instance (Anaconda), I seem to always get a kernel crash (segmentation fault) when I try and actually use or create one of my custom filters.

To strip everything back to basics I generated a vanilla external module, using only default values with:

python -m cookiecutter gh:InsightSoftwareConsortium/ITKModuleTemplate

I then built the wheels as described and installed them into the virtual environment.

Using the following basic python script below results in a seg fault,

import itk
InputType = itk.Image[itk.F,2]
OutputType = itk.Image[itk.F,2]
test = itk.MinimalStandardRandomVariateGenerator.New()

I get the same result if I try and create any of the classes defined in ITKModuleTemplate, however I can successfully create standard itk filters.

After running the script with gdb I see that it crashes in the call as follows:

#1  0x00007fffe7405373 in PyInit__ModuleTemplatePython () from /home/tho78s/anaconda3/lib/python3.6/site-packages/itk/Configuration/../_ModuleTemplatePython.so

I'm currently out of ideas as to where the problem lies and I seem to get the identical problem in Windows too.

Any help or pointers in to what is going wrong would be greatly appreciated!

I you want any extra info, feel free to contact me.

Regards,

Darren

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://itk.org/pipermail/insight-users/attachments/20180712/9ab6de77/attachment.html>

From srbn.ghosh99 at gmail.com  Fri Jul 13 12:07:10 2018
From: srbn.ghosh99 at gmail.com (Shrabani Ghosh)
Date: Fri, 13 Jul 2018 09:07:10 -0700 (MST)
Subject: [ITK-users] How to convert vtk data to vtp data
Message-ID: <1531498030634-0.post@n2.nabble.com>

I want to convert my vtk to vtp data. Is there any example available for the
conversion. 

Please suggest. 



--
Sent from: http://itk-insight-users.2283740.n2.nabble.com/

From gunjan_naik at persistent.com  Sun Jul 15 14:53:53 2018
From: gunjan_naik at persistent.com (Gunjan Naik)
Date: Sun, 15 Jul 2018 18:53:53 +0000
Subject: [ITK-users] Undefined function SaveMHDData
Message-ID: <MAXPR0101MB1484F1C9F4C29F18FCCDFB7DFB5E0@MAXPR0101MB1484.INDPRD01.PROD.OUTLOOK.COM>

Hi,


I wanted to build the Glistr library, for brain tumor segmentation.


URL:http://www.med.upenn.edu/sbia/glistr.html

GLISTR | Section for Biomedical Image Analysis (SBIA ...<http://www.med.upenn.edu/sbia/glistr.html>
www.med.upenn.edu
The Section for Biomedical Image Analysis (SBIA), part of the Center of Biomedical Image Computing and Analytics ? CBICA, is devoted to the development of computer-based image analysis methods, and their application to a wide variety of clinical research studies.


While building that, I got the following error:

'Linking CXX executable EvaluateQ
CMakeFiles/EvaluateQ.dir/EvaluateQ.cpp.o: In function `int SaveMHDData<float>(char const*, char const*, float****, float****, float****, int, int, int, float, float, float, float, float, float)':
EvaluateQ.cpp:(.text._Z11SaveMHDDataIfEiPKcS1_PPPPT_S6_S6_iiiffffff[_Z11SaveMHDDataIfEiPKcS1_PPPPT_S6_S6_iiiffffff]+0x9c): undefined reference to `MetaImage::MetaImage(int, int, int, float, float, float, MET_ValueEnumType, int, void*)'
collect2: error: ld returned 1 exit status'


Is there any function 'SaveMHDData' in the ITK library, for which I have to set the parameters, while building ITK from source?


Thanks and Regards,

Gunjan Naik
DISCLAIMER
==========
This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://itk.org/pipermail/insight-users/attachments/20180715/59979726/attachment.html>

From jhlegarreta at vicomtech.org  Mon Jul 16 02:22:14 2018
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Mon, 16 Jul 2018 08:22:14 +0200
Subject: [ITK-users] How to convert vtk data to vtp data
In-Reply-To: <1531498030634-0.post@n2.nabble.com>
References: <1531498030634-0.post@n2.nabble.com>
Message-ID: <CAAKhGh8ajzSTKnqzam0WAzxRkR6kjWy6uJARUYgxPNd1rhPPrQ@mail.gmail.com>

Hi Shrabani,
these file formats are used by VTK. You are more likely to get a
better answer if you post to the VTK mailing list:
https://www.vtk.org/mailing-lists/

Also, note that ITK has transitioned to the discourse.itk.org
discussion site. Whenever you need to post a question about ITK,
please use the discourse.itk.org site.


Thanks,
JON HAITZ

--


On 13 July 2018 at 18:07, Shrabani Ghosh <srbn.ghosh99 at gmail.com> wrote:
> I want to convert my vtk to vtp data. Is there any example available for the
> conversion.
>
> Please suggest.
>
>
>
> --
> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
> The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> https://itk.org/mailman/listinfo/insight-users

From dzenanz at gmail.com  Mon Jul 16 12:35:28 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 16 Jul 2018 12:35:28 -0400
Subject: [ITK-users] ITKModuleTemplate and external modules for use with
 python
In-Reply-To: <45eec90025e2442c85429ef978da1ecd@exch3-mel.nexus.csiro.au>
References: <45eec90025e2442c85429ef978da1ecd@exch3-mel.nexus.csiro.au>
Message-ID: <CAPf2UMRjbkX4ZsdBMLzi3UynTMFC5kjNK+1V6SWu__6CpcK7VA@mail.gmail.com>

Hi Darren,

can you please re-post this question on the forum
<https://discourse.itk.org/>? Many of us were on vacation in the last few
weeks.

Regards,
D?enan

On Thu, Jul 12, 2018 at 7:47 AM <Darren.Thompson at csiro.au> wrote:

> Hi All,
>
>
>
> I?m revisiting making my own external ITK module (for use in Python) after
> an initial attempt a while back. This time I?ve managed to get much further
> and have managed to successfully create python wheels following the
> directions on
> https://github.com/InsightSoftwareConsortium/ITKPythonPackage/blob/master/docs/Build_ITK_Module_Python_packages.rst
>  , I?ve created Windows wheels via AppVeyor and linux wheels with CircleCI
> in addition to locally built versions via the docker based method. All
> tests are passed successfully.
>
>
>
> However, after installing them with pip in a fresh virtual environment in
> a Python 3.6 instance (Anaconda), I seem to always get a kernel crash
> (segmentation fault) when I try and actually use or create one of my custom
> filters.
>
>
>
> To strip everything back to basics I generated a vanilla external module,
> using only default values with:
>
>
>
> python -m cookiecutter gh:InsightSoftwareConsortium/ITKModuleTemplate
>
>
>
> I then built the wheels as described and installed them into the virtual
> environment.
>
>
>
> Using the following basic python script below results in a seg fault,
>
>
>
> import itk
>
> InputType = itk.Image[itk.F,2]
>
> OutputType = itk.Image[itk.F,2]
>
> test = itk.MinimalStandardRandomVariateGenerator.New()
>
>
>
> I get the same result if I try and create any of the classes defined in
> ITKModuleTemplate, however I can successfully create standard itk filters.
>
>
>
> After running the script with gdb I see that it crashes in the call as
> follows:
>
>
>
> #1  0x00007fffe7405373 in PyInit__ModuleTemplatePython () from
> /home/tho78s/anaconda3/lib/python3.6/site-packages/itk/Configuration/../_ModuleTemplatePython.so
>
>
>
> I?m currently out of ideas as to where the problem lies and I seem to get
> the identical problem in Windows too.
>
>
>
> Any help or pointers in to what is going wrong would be greatly
> appreciated!
>
>
>
> I you want any extra info, feel free to contact me.
>
>
>
> Regards,
>
>
>
> Darren
>
>
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> https://itk.org/mailman/listinfo/insight-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://itk.org/pipermail/insight-users/attachments/20180716/465a1ad2/attachment.html>

From dzenanz at gmail.com  Mon Jul 16 12:40:58 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 16 Jul 2018 12:40:58 -0400
Subject: [ITK-users] Undefined function SaveMHDData
In-Reply-To: <MAXPR0101MB1484F1C9F4C29F18FCCDFB7DFB5E0@MAXPR0101MB1484.INDPRD01.PROD.OUTLOOK.COM>
References: <MAXPR0101MB1484F1C9F4C29F18FCCDFB7DFB5E0@MAXPR0101MB1484.INDPRD01.PROD.OUTLOOK.COM>
Message-ID: <CAPf2UMT2WXt04wWB0gqKptNZJF_jVDwTO2tyTBEoiJ+38J4NMw@mail.gmail.com>

SaveMHDData is a function in glistr, and a constructor for MetaImage which
it invokes is not available during link stage. It could be something wrong
with that library's build system, you could have set up something in a
wrong way, or the library is relying on a constructor signature which is no
longer available.

MetaImage saw some precision-related update in the last year I think, and
that might have changed the constructor signature. You could try with an
older version of ITK, e.g. 4.11.

Regards,
D?enan

On Sun, Jul 15, 2018 at 3:04 PM Gunjan Naik <gunjan_naik at persistent.com>
wrote:

> Hi,
>
>
> I wanted to build the Glistr library, for brain tumor segmentation.
>
>
> URL:http://www.med.upenn.edu/sbia/glistr.html
> GLISTR | Section for Biomedical Image Analysis (SBIA ...
> <http://www.med.upenn.edu/sbia/glistr.html>
> www.med.upenn.edu
> The Section for Biomedical Image Analysis (SBIA), part of the Center of
> Biomedical Image Computing and Analytics ? CBICA, is devoted to the
> development of computer-based image analysis methods, and their application
> to a wide variety of clinical research studies.
>
> While building that, I got the following error:
>
> 'Linking CXX executable EvaluateQ
> CMakeFiles/EvaluateQ.dir/EvaluateQ.cpp.o: In function `int
> SaveMHDData<float>(char const*, char const*, float****, float****,
> float****, int, int, int, float, float, float, float, float, float)':
> EvaluateQ.cpp:(.text._Z11SaveMHDDataIfEiPKcS1_PPPPT_S6_S6_iiiffffff[_Z11SaveMHDDataIfEiPKcS1_PPPPT_S6_S6_iiiffffff]+0x9c):
> undefined reference to `MetaImage::MetaImage(int, int, int, float, float,
> float, MET_ValueEnumType, int, void*)'
> collect2: error: ld returned 1 exit status'
>
>
> Is there any function 'SaveMHDData' in the ITK library, for which I have
> to set the parameters, while building ITK from source?
>
>
> Thanks and Regards,
>
> Gunjan Naik
> DISCLAIMER
> ==========
> This e-mail may contain privileged and confidential information which is
> the property of Persistent Systems Ltd. It is intended only for the use of
> the individual or entity to which it is addressed. If you are not the
> intended recipient, you are not authorized to read, retain, copy, print,
> distribute or use this message. If you have received this communication in
> error, please notify the sender and delete all copies of this message.
> Persistent Systems Ltd. does not accept any liability for virus infected
> mails.
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> https://itk.org/mailman/listinfo/insight-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://itk.org/pipermail/insight-users/attachments/20180716/e5c42269/attachment.html>

From gunjan_naik at persistent.com  Tue Jul 17 06:30:46 2018
From: gunjan_naik at persistent.com (Gunjan Naik)
Date: Tue, 17 Jul 2018 10:30:46 +0000
Subject: [ITK-users] Undefined function SaveMHDData
In-Reply-To: <CAPf2UMT2WXt04wWB0gqKptNZJF_jVDwTO2tyTBEoiJ+38J4NMw@mail.gmail.com>
References: <MAXPR0101MB1484F1C9F4C29F18FCCDFB7DFB5E0@MAXPR0101MB1484.INDPRD01.PROD.OUTLOOK.COM>,
 <CAPf2UMT2WXt04wWB0gqKptNZJF_jVDwTO2tyTBEoiJ+38J4NMw@mail.gmail.com>
Message-ID: <MAXPR0101MB148471F1596545DD8DAE1DCBFB5C0@MAXPR0101MB1484.INDPRD01.PROD.OUTLOOK.COM>

Thanks D?enan Zuki?,


As per your guideline, I build an older ITK with version 4.7.2. And set the flags for MetaImage using ImageIO. The Glistr has been built.


Regards,

Gunjan Naik

________________________________
From: D?enan Zuki? <dzenanz at gmail.com>
Sent: Monday, July 16, 2018 10:10 PM
To: Gunjan Naik
Cc: Insight-users
Subject: Re: [ITK-users] Undefined function SaveMHDData

SaveMHDData is a function in glistr, and a constructor for MetaImage which it invokes is not available during link stage. It could be something wrong with that library's build system, you could have set up something in a wrong way, or the library is relying on a constructor signature which is no longer available.

MetaImage saw some precision-related update in the last year I think, and that might have changed the constructor signature. You could try with an older version of ITK, e.g. 4.11.

Regards,
D?enan

On Sun, Jul 15, 2018 at 3:04 PM Gunjan Naik <gunjan_naik at persistent.com<mailto:gunjan_naik at persistent.com>> wrote:

Hi,


I wanted to build the Glistr library, for brain tumor segmentation.


URL:http://www.med.upenn.edu/sbia/glistr.html

GLISTR | Section for Biomedical Image Analysis (SBIA ...<http://www.med.upenn.edu/sbia/glistr.html>
www.med.upenn.edu<http://www.med.upenn.edu>
The Section for Biomedical Image Analysis (SBIA), part of the Center of Biomedical Image Computing and Analytics ? CBICA, is devoted to the development of computer-based image analysis methods, and their application to a wide variety of clinical research studies.


While building that, I got the following error:

'Linking CXX executable EvaluateQ
CMakeFiles/EvaluateQ.dir/EvaluateQ.cpp.o: In function `int SaveMHDData<float>(char const*, char const*, float****, float****, float****, int, int, int, float, float, float, float, float, float)':
EvaluateQ.cpp:(.text._Z11SaveMHDDataIfEiPKcS1_PPPPT_S6_S6_iiiffffff[_Z11SaveMHDDataIfEiPKcS1_PPPPT_S6_S6_iiiffffff]+0x9c): undefined reference to `MetaImage::MetaImage(int, int, int, float, float, float, MET_ValueEnumType, int, void*)'
collect2: error: ld returned 1 exit status'


Is there any function 'SaveMHDData' in the ITK library, for which I have to set the parameters, while building ITK from source?


Thanks and Regards,

Gunjan Naik

DISCLAIMER
==========
This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.
The ITK community is transitioning from this mailing list to discourse.itk.org<http://discourse.itk.org>. Please join us there!
________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
https://itk.org/mailman/listinfo/insight-users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://itk.org/pipermail/insight-users/attachments/20180717/f8b11c1c/attachment.html>

From srbn.ghosh99 at gmail.com  Thu Jul 19 18:36:34 2018
From: srbn.ghosh99 at gmail.com (Shrabani Ghosh)
Date: Thu, 19 Jul 2018 15:36:34 -0700 (MST)
Subject: [ITK-users] Split 3D image one image into two parts
Message-ID: <1532039794697-0.post@n2.nabble.com>

Hi,

I have a 3D image to use it for a machine learning problem. But when I am
trying to run it , it's running out of memory. Is there any way to spit the
3D image into two parts?
Because I have tried to split the 3D image into 2D slices.  But 2D slices
are not the same as the original image slice of the 3D image anymore. 



--
Sent from: http://itk-insight-users.2283740.n2.nabble.com/

From pablo.hernandez.cerdan at outlook.com  Fri Jul 20 02:36:29 2018
From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=)
Date: Fri, 20 Jul 2018 06:36:29 +0000
Subject: [ITK-users] Split 3D image one image into two parts
In-Reply-To: <1532039794697-0.post@n2.nabble.com>
References: <1532039794697-0.post@n2.nabble.com>
Message-ID: <AM5PR03MB3124513EC5C6F498A2FA409AD6510@AM5PR03MB3124.eurprd03.prod.outlook.com>

Hi Shrabani,
I think you already asked this exact same question in a post in discourse [0] some time ago!

As mentioned there, you can use a CropImageFilter or a ExtractImageFilter providing a 3D region.

[0]: https://discourse.itk.org/t/how-to-crop-a-3d-image-with-a-specified-size/715

On Thu, Jul 19, 2018 at 6:36 PM, Shrabani Ghosh <srbn.ghosh99 at gmail.com<mailto:srbn.ghosh99 at gmail.com>> wrote:
Hi,

I have a 3D image to use it for a machine learning problem. But when I am
trying to run it , it's running out of memory. Is there any way to spit the
3D image into two parts?
Because I have tried to split the 3D image into 2D slices.  But 2D slices
are not the same as the original image slice of the 3D image anymore.



--
Sent from: http://itk-insight-users.2283740.n2.nabble.com/
The ITK community is transitioning from this mailing list to discourse.itk.org<http://discourse.itk.org>. Please join us there!
________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
https://itk.org/mailman/listinfo/insight-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://itk.org/pipermail/insight-users/attachments/20180720/2a02b844/attachment.html>

From pablo.hernandez.cerdan at outlook.com  Fri Jul 20 02:36:30 2018
From: pablo.hernandez.cerdan at outlook.com (=?utf-8?B?UGFibG8gSGVybsOhbmRleg==?=)
Date: Fri, 20 Jul 2018 06:36:30 +0000
Subject: [ITK-users] Split 3D image one image into two parts
In-Reply-To: <1532039794697-0.post@n2.nabble.com>
References: <1532039794697-0.post@n2.nabble.com>
Message-ID: <AM5PR03MB312498D72A101BCEF944C3F1D6510@AM5PR03MB3124.eurprd03.prod.outlook.com>

Hi Shrabani,
I think you already asked this exact same question in a post in discourse [0] some time ago!

As mentioned there, you can use a CropImageFilter or a ExtractImageFilter providing a 3D region.

[0]: https://discourse.itk.org/t/how-to-crop-a-3d-image-with-a-specified-size/715

On Thu, Jul 19, 2018 at 6:36 PM, Shrabani Ghosh <srbn.ghosh99 at gmail.com<mailto:srbn.ghosh99 at gmail.com>> wrote:
Hi,

I have a 3D image to use it for a machine learning problem. But when I am
trying to run it , it's running out of memory. Is there any way to spit the
3D image into two parts?
Because I have tried to split the 3D image into 2D slices.  But 2D slices
are not the same as the original image slice of the 3D image anymore.



--
Sent from: http://itk-insight-users.2283740.n2.nabble.com/
The ITK community is transitioning from this mailing list to discourse.itk.org<http://discourse.itk.org>. Please join us there!
________________________________
Powered by www.kitware.com<http://www.kitware.com>

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
https://itk.org/mailman/listinfo/insight-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://itk.org/pipermail/insight-users/attachments/20180720/f74b3a96/attachment.html>

From srbn.ghosh99 at gmail.com  Thu Jul 26 10:47:51 2018
From: srbn.ghosh99 at gmail.com (Shrabani Ghosh)
Date: Thu, 26 Jul 2018 07:47:51 -0700 (MST)
Subject: [ITK-users] Combine Polydata
Message-ID: <1532616471776-0.post@n2.nabble.com>

I want to combine two vtk file together so that they can stick together. But
after combining them I can see that they did stick together with same world
coordinate. I used this code. How to do that?

https://itk.org/Wiki/VTK/Examples/Cxx/Filtering/CombinePolyData

<http://itk-insight-users.2283740.n2.nabble.com/file/t396636/Capture.png> 




--
Sent from: http://itk-insight-users.2283740.n2.nabble.com/

From dzenanz at gmail.com  Thu Jul 26 11:29:03 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 26 Jul 2018 11:29:03 -0400
Subject: [ITK-users] Combine Polydata
In-Reply-To: <1532616471776-0.post@n2.nabble.com>
References: <1532616471776-0.post@n2.nabble.com>
Message-ID: <CAPf2UMTkq_50B3WUUG09X9mfamYgoXewZwkfcKNp3W2Eo+V2wQ@mail.gmail.com>

Hi Shrabani,

I think you might have posted to the wrong list. Perhaps you wanted
vtk-users <https://www.vtk.org/mailman/listinfo/vtkusers>?

Also, your question is not clear enough. Did that code work or not? If not,
how was the result different from your expectation.

Regards,
D?enan

On Thu, Jul 26, 2018 at 10:47 AM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
wrote:

> I want to combine two vtk file together so that they can stick together.
> But
> after combining them I can see that they did stick together with same world
> coordinate. I used this code. How to do that?
>
> https://itk.org/Wiki/VTK/Examples/Cxx/Filtering/CombinePolyData
>
> <http://itk-insight-users.2283740.n2.nabble.com/file/t396636/Capture.png>
>
>
>
>
> --
> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> https://itk.org/mailman/listinfo/insight-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://itk.org/pipermail/insight-users/attachments/20180726/ed12edb8/attachment.html>

From dzenanz at gmail.com  Thu Jul 26 11:42:49 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 26 Jul 2018 11:42:49 -0400
Subject: [ITK-users] Combine Polydata
In-Reply-To: <CADHEK9-ur0LqOfJZf7Ksjmz-C+tdTvDCRFSsLtrjfUC0E9Ax6Q@mail.gmail.com>
References: <1532616471776-0.post@n2.nabble.com>
 <CAPf2UMTkq_50B3WUUG09X9mfamYgoXewZwkfcKNp3W2Eo+V2wQ@mail.gmail.com>
 <CADHEK9-ur0LqOfJZf7Ksjmz-C+tdTvDCRFSsLtrjfUC0E9Ax6Q@mail.gmail.com>
Message-ID: <CAPf2UMTRJx8rkAGE6D+bVmwa4WQdnMwScRjhzkus9wJJ9etMeg@mail.gmail.com>

You probably need to supply the transform to have the proper alignment
after merging the meshes.

On Thu, Jul 26, 2018 at 11:37 AM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
wrote:

> Okay. I can post it in the VTK users. The code did not as I wanted. I want
> the two polydata will overlap onto each other.. and fit together.    Like
> image 1, 2 combine together and created 3.
>
>
> On Thu, Jul 26, 2018 at 11:29 AM D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> Hi Shrabani,
>>
>> I think you might have posted to the wrong list. Perhaps you wanted
>> vtk-users <https://www.vtk.org/mailman/listinfo/vtkusers>?
>>
>> Also, your question is not clear enough. Did that code work or not? If
>> not, how was the result different from your expectation.
>>
>> Regards,
>> D?enan
>>
>> On Thu, Jul 26, 2018 at 10:47 AM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
>> wrote:
>>
>>> I want to combine two vtk file together so that they can stick together.
>>> But
>>> after combining them I can see that they did stick together with same
>>> world
>>> coordinate. I used this code. How to do that?
>>>
>>> https://itk.org/Wiki/VTK/Examples/Cxx/Filtering/CombinePolyData
>>>
>>> <http://itk-insight-users.2283740.n2.nabble.com/file/t396636/Capture.png>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
>>> The ITK community is transitioning from this mailing list to
>>> discourse.itk.org. Please join us there!
>>> ________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> https://itk.org/mailman/listinfo/insight-users
>>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://itk.org/pipermail/insight-users/attachments/20180726/2b55d28c/attachment.html>

From dzenanz at gmail.com  Thu Jul 26 11:51:10 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 26 Jul 2018 11:51:10 -0400
Subject: [ITK-users] Combine Polydata
In-Reply-To: <CADHEK9-Sp1NZDP0Vpu-Mvq7TA8_XcXT5zK-TS+fZRcgMZiM6hg@mail.gmail.com>
References: <1532616471776-0.post@n2.nabble.com>
 <CAPf2UMTkq_50B3WUUG09X9mfamYgoXewZwkfcKNp3W2Eo+V2wQ@mail.gmail.com>
 <CADHEK9-ur0LqOfJZf7Ksjmz-C+tdTvDCRFSsLtrjfUC0E9Ax6Q@mail.gmail.com>
 <CAPf2UMTRJx8rkAGE6D+bVmwa4WQdnMwScRjhzkus9wJJ9etMeg@mail.gmail.com>
 <CADHEK9-Sp1NZDP0Vpu-Mvq7TA8_XcXT5zK-TS+fZRcgMZiM6hg@mail.gmail.com>
Message-ID: <CAPf2UMTjrpvh7+gVgv6EAtYnCk+27ymMJN6QyCUsNMmc4DWA8g@mail.gmail.com>

 How about this
<https://www.vtk.org/Wiki/VTK/Examples/Cxx/Filtering/TransformPolyData>?

On Thu, Jul 26, 2018 at 11:49 AM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
wrote:

> Okay. Is there any similar kind of example  given vtk?
>
> On Thu, Jul 26, 2018 at 11:43 AM D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> You probably need to supply the transform to have the proper alignment
>> after merging the meshes.
>>
>> On Thu, Jul 26, 2018 at 11:37 AM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
>> wrote:
>>
>>> Okay. I can post it in the VTK users. The code did not as I wanted. I
>>> want the two polydata will overlap onto each other.. and fit together.
>>> Like image 1, 2 combine together and created 3.
>>>
>>>
>>> On Thu, Jul 26, 2018 at 11:29 AM D?enan Zuki? <dzenanz at gmail.com> wrote:
>>>
>>>> Hi Shrabani,
>>>>
>>>> I think you might have posted to the wrong list. Perhaps you wanted
>>>> vtk-users <https://www.vtk.org/mailman/listinfo/vtkusers>?
>>>>
>>>> Also, your question is not clear enough. Did that code work or not? If
>>>> not, how was the result different from your expectation.
>>>>
>>>> Regards,
>>>> D?enan
>>>>
>>>> On Thu, Jul 26, 2018 at 10:47 AM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
>>>> wrote:
>>>>
>>>>> I want to combine two vtk file together so that they can stick
>>>>> together. But
>>>>> after combining them I can see that they did stick together with same
>>>>> world
>>>>> coordinate. I used this code. How to do that?
>>>>>
>>>>> https://itk.org/Wiki/VTK/Examples/Cxx/Filtering/CombinePolyData
>>>>>
>>>>> <
>>>>> http://itk-insight-users.2283740.n2.nabble.com/file/t396636/Capture.png>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
>>>>> The ITK community is transitioning from this mailing list to
>>>>> discourse.itk.org. Please join us there!
>>>>> ________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>> http://www.kitware.com/products/protraining.php
>>>>>
>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> https://itk.org/mailman/listinfo/insight-users
>>>>>
>>>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://itk.org/pipermail/insight-users/attachments/20180726/57fec55a/attachment.html>