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Dženan Zukić | 1 Aug 2012 12:40
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Re: [OSX] Include ITK in a .pro Qt Creator Project [Partially Solved]

If you are just starting, better go with CMake straight away. And here is an example CMakeLists.txt:

cmake_minimum_required(VERSION 2.6)

PROJECT(Spine CXX)

find_path( EIGEN_DIR Eigen DOC "A path to Eigen libaray, a linear algebra solver" )
INCLUDE_DIRECTORIES( ${EIGEN_DIR} )

FIND_PACKAGE(ITK REQUIRED)
INCLUDE(${ITK_USE_FILE})

FIND_PACKAGE(VTK REQUIRED)
INCLUDE(${VTK_USE_FILE})

FIND_PACKAGE(Qt4)
SET(QT_USE_QTOPENGL 1)
SET(QT_USE_QTDESIGNER ON)
INCLUDE(${QT_USE_FILE})
INCLUDE_DIRECTORIES(${QT_INCLUDE_DIR})
   
SET(SAMPLE_SRCS
    Spine.cxx
    mainWindow.cpp
    slicePainter.cpp
    vec3.h
    MainLogic.cpp
    declarations.h
    butterfly.cpp
    qeUtil.cpp
    LHstuff.cpp
    vertebra.h
    vertebra.cpp
    polyfit.cpp
    vtkOBJWriter.cxx
    )
SET(SAMPLE_MOC_HDRS mainWindow.h MainLogic.h slicePainter.h)
SET(SAMPLE_UIS mainWindow.ui slicePainter.ui)
SET(SAMPLE_RCS mainWindow.qrc)

QT4_ADD_RESOURCES( SAMPLE_RC_SRCS ${SAMPLE_RCS} )
QT4_WRAP_UI( SAMPLE_UI_HDRS ${SAMPLE_UIS} )
QT4_WRAP_CPP( SAMPLE_MOC_SRCS ${SAMPLE_MOC_HDRS} )
  
ADD_EXECUTABLE(Spine ${SAMPLE_SRCS} ${SAMPLE_MOC_HDRS} ${SAMPLE_MOC_SRCS} ${SAMPLE_RC_SRCS} ${SAMPLE_UI_HDRS})

TARGET_LINK_LIBRARIES(Spine ${QT_LIBRARIES})
TARGET_LINK_LIBRARIES(Spine ${ITK_LIBRARIES})
TARGET_LINK_LIBRARIES(Spine ${VTK_LIBRARIES} QVTK)

On Tue, Jul 31, 2012 at 10:21 PM, jelemans <jelemans-TxZPKD6LPqNBDgjK7y7TUQ@public.gmane.org> wrote:
I'm just starting a QT +ITK project. Would you be willing to post your .pro
file or an example to show how to get started?

Did you solve the problem?

TIA.



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Luis Ibanez | 1 Aug 2012 15:47
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Re: Information about ITK Segmentation

Hi Nuno,


You can use any image viewer in order to manually pick 
points in the image. Please note that those points are
pixel index coordinates (integer numbers in the image 
grid), as opposed to physical coordinates in the actual
space of the anatomy.

You could use the ImageViewer application from ITKApps,
or applications such as Slicer and VolView, to pick points
that are seeds.

Note also, that the points are not expected to be in the
boundaries of the object, but in the middle of it, and will
be used to grow a level set from there.


   Hope this helps,


       Luis


---------------------------------------
On Tue, Jul 31, 2012 at 11:54 AM, Nuno Catarino <ncatarino87 <at> gmail.com> wrote:
Dear Sir Luis Ibanez,


I'm using GeodesicActiveContourImageFilter.cxx to target an ultrasound image. I would like to know where points are extracted from the contour of the binary image, or is there another way to remove these points to a txt file.

I just need the points.

Grateful for the attention.

With Best Regards

Nuno Catarino
 

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amir_k | 1 Aug 2012 17:02
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writing mesh segmentation result (based on the example DeformableModel2)


Hello,

1) I am trying to write the output from the DeformableMesh3DFilter. My
pipeline is based on the example from DeformableModel2.cxx.

Here is what I do at the moment:

        deformableModelFilter->Update();
		qDebug() <<"Done segmenting with Deformable Model filter"<<endl;

	//write the segmented  volume in mhd file	
	typedef DeformableFilterType::OutputMeshType LabeledMeshType;

	typedef itk::ImageFileWriter<LabeledMeshType> writerType4;
	writerType4::Pointer writer4 = writerType4::New();
	writer4->SetFileName("output_DM.mhd"); //("input.mha");
	writer4->SetInput(deformableModelFilter->GetOutput());
	writer4->SetImageIO(itk::MetaImageIO::New());
	try {
		writer4->Update();
	}
	catch (itk::ExceptionObject& ex){
		qDebug()<<ex.what()<<endl;
	}

I get an error :
error C2039: 'ImageDimension' : is not a member of 'itk::Mesh<TPixelType>'
C:\Program Files\ITK\include\ITK-4.0\itkImageFileWriter.h	172

2)Otherwise, I would to visualize this by passing this segmentation output
to VTK pipeline with the reference of Seamless VTK-ITK pipeline. here are
the code lines :

        /*------------ITK to VTK pipeline connection-----------*/
	vtkKWImage *kwImage = vtkKWImage::New();
	kwImage->SetITKImageBase(deformableModelFilter->GetOutput());

		qDebug()<<"Connecting ITK pipeline to VTK pipeline"<<endl;
	
	vtkImageData *vtkImage = kwImage->GetVTKImage();

but here I get as error:
error C2664: 'vtkKWImage::SetITKImageBase' : cannot convert parameter 1 from
'itk::Mesh<TPixelType> *' to 'vtkKWImage::ImageBaseType *'	c:\Documents and
Settings\amir\Bureau\CTScan3D\CTScan3D\ctscan3d.cpp	587

Thank you for any hints.

best,
amir

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Prateep Mukherjee | 1 Aug 2012 21:49
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is there a way to install ITK-4.1.0 on Mac through Macports

Hi,

  I have been trying to install ITK-4.1.0 on Mac Snow Leopard through Macports. But this(http://www.macports.org/ports.php?by=category&substr=math&page=1&pagesize=500) says that the latest version is 3.16.0.

 Is there a way to install 4.1.0 through CMake or XCode ?

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Prateep.

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Dr. Tim Allman | 2 Aug 2012 00:35
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Re: is there a way to install ITK-4.1.0 on Mac through Macports

Actually the latest version is 4.2.0.

You need to download and expand it. Read the file "GettingStarted.txt". It contains the information you need.

Tim



On 12-08-01 03:49 PM, Prateep Mukherjee wrote:
Hi,

  I have been trying to install ITK-4.1.0 on Mac Snow Leopard through Macports. But this(http://www.macports.org/ports.php?by=category&substr=math&page=1&pagesize=500) says that the latest version is 3.16.0.

 Is there a way to install 4.1.0 through CMake or XCode ?

--
Thanks,
Prateep.



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| 2 Aug 2012 05:10
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A problem about extract the region of interest

HI ALL

i'm doing my project using ITK. but i got a problem about the extract of 3D image.

i'm using vtkRegionofInterestImageFilter. follow the example:

ImageType::IndexType start;
start[0] = …
start[1] = …
start[2] = …

ImageType::SizeType size;
size[0] = …
size[1] = …
size[2] = …

ImageType::RegionType desiredRegion;
desiredRegion.SetSize(size);
desiredRegion.SetIndex(start);

BUT, i hope that the start point that i gave can be the center point of the cube. not the cornor.

what should i do . thank u.

--
Ryuu

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Kiên Kiêu | 2 Aug 2012 10:40
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update image filter

Hi,

I have a question regarding image filter updating. I have a pipeline of 
image filters. At some point, I update one of them using 
UpdateLargestPossibleRegion method. I need to know whether the filter 
has been executed or not (it may have not been executed it no anterior 
filter in the pipeline has been modified since the previous update). 
What method should I use?

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Ale | 2 Aug 2012 10:45
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Re: [OSX] Include ITK in a .pro Qt Creator Project [Partially Solved]

Hi all,

sorry for late: I didn't see the answers since it's a long time I've written.

I don't like CMake because you lost all Creator features if you use it. Once you have your .pro project you
should include things like that (take care about absolute paths!) at the bottom of your project:

win32:CONFIG(release, debug|release): LIBS += -L$$PWD/../../../../../../usr/local/lib/release/ -lITKCommon-4
else:win32:CONFIG(debug, debug|release): LIBS +=
-L$$PWD/../../../../../../usr/local/lib/debug/ -lITKCommon-4
else:symbian: LIBS += -lITKCommon-4
else:unix: LIBS += -L/usr/local/lib/ \
-lITKBiasCorrection-4.1 \
-lITKBioCell-4.1 \
-lITKCommon-4.1 \
-lITKDeprecated-4.1 \
-lITKDICOMParser-4.1 \
-lITKEXPAT-4.1 \
-lITKFEM-4.1 \
                                     -lITKgiftiio-4.1 \
                                        -litkhdf5-4.1 \
                                        -litkhdf5_cpp-4.1 \
                                        -lITKIOBioRad-4.1 \
                                        -lITKIOBMP-4.1 \
                                        -lITKIOCSV-4.1 \
                    -lITKIOGDCM-4.1 \
                    -lITKGDCM-4.1\
                                        -lITKIOGE-4.1 \
                                        -lITKIOGIPL-4.1 \
                                        -lITKIOHDF5-4.1 \
                    -lITKIOImageBase-4.1 \
                    -lITKIOIPL-4.1 \
                    -lITKIOJPEG-4.1 \
-lITKIOLSM-4.1 \
                    -lITKIOMesh-4.1 \
                    -lITKIOMeta-4.1 \
                    -lITKIONIFTI-4.1 \
                                        -lITKIONRRD-4.1 \
                                        -lITKIOPNG-4.1 \
                                        -lITKIOSiemens-4.1 \
                    -lITKIOSpatialObjects-4.1 \
-lITKIOStimulate-4.1 \
                    -lITKIOTIFF-4.1 \
                    -lITKIOTransformBase-4.1 \
                                        -lITKIOTransformHDF5-4.1 \
                                        -lITKIOTransformInsightLegacy-4.1 \
                                        -lITKIOTransformMatlab-4.1 \
                                        -lITKIOVTK-4.1 \
                    -lITKIOXML-4.1 \
                    -litkjpeg-4.1 \
                                        -lITKKLMRegionGrowing-4.1 \
                                        -lITKLabelMap-4.1 \
                                        -lITKMesh-4.1 \
                    -lITKMetaIO-4.1 \
                    -litkNetlibSlatec-4.1 \
                                        -lITKniftiio-4.1 \
                                        -lITKNrrdIO-4.1 \
                    -lITKOptimizers-4.1 \
                    -lITKOptimizersv4-4.1 \
                    -lITKPath-4.1 \
                    -litkpng-4.1 \
                    -lITKStatistics-4.1 \
                                        -lITKPolynomials-4.1 \
                                        -lITKQuadEdgeMesh-4.1 \
                                        -lITKReview-4.1 \
                                        -lITKSpatialObjects-4.1 \
                                        -lITKStatistics-4.1 \
                                        -litksys-4.1 \
                                        -litktiff-4.1 \
                                        -litkv3p_lsqr-4.1 \
                                        -litkv3p_netlib-4.1 \
                                        -litkvcl-4.1 \
                                        -lITKVideoCore-4.1 \
                                        -lITKVideoIO-4.1 \
                                        -litkvnl-4.1 \
                                        -lITKVNLInstantiation-4.1 \
                                        -litkvnl_algo-4.1 \
                                        -lITKVTK-4.1 \
                                        -lITKWatersheds-4.1 \
                                        -litkzlib-4.1 \
                                        -lITKznz-4.1

#set MAC CoreFoundation includes
mac: LIBS += -framework CoreFoundation

INCLUDEPATH += /usr/local/include/ITK-4.1
DEPENDPATH += /usr/local/include/ITK-4.1

Il giorno 01/ago/2012, alle ore 12.40, Dženan Zukić ha scritto:

> If you are just starting, better go with CMake straight away. And here is an example CMakeLists.txt:
> 
> cmake_minimum_required(VERSION 2.6)
> 
> PROJECT(Spine CXX)
> 
> find_path( EIGEN_DIR Eigen DOC "A path to Eigen libaray, a linear algebra solver" )
> INCLUDE_DIRECTORIES( ${EIGEN_DIR} )
> 
> FIND_PACKAGE(ITK REQUIRED)
> INCLUDE(${ITK_USE_FILE})
> 
> FIND_PACKAGE(VTK REQUIRED)
> INCLUDE(${VTK_USE_FILE})
> 
> FIND_PACKAGE(Qt4)
> SET(QT_USE_QTOPENGL 1)
> SET(QT_USE_QTDESIGNER ON)
> INCLUDE(${QT_USE_FILE})
> INCLUDE_DIRECTORIES(${QT_INCLUDE_DIR})
>    
> SET(SAMPLE_SRCS
>     Spine.cxx
>     mainWindow.cpp
>     slicePainter.cpp
>     vec3.h
>     MainLogic.cpp
>     declarations.h
>     butterfly.cpp
>     qeUtil.cpp
>     LHstuff.cpp
>     vertebra.h
>     vertebra.cpp
>     polyfit.cpp
>     vtkOBJWriter.cxx
>     )
> SET(SAMPLE_MOC_HDRS mainWindow.h MainLogic.h slicePainter.h)
> SET(SAMPLE_UIS mainWindow.ui slicePainter.ui)
> SET(SAMPLE_RCS mainWindow.qrc)
> 
> QT4_ADD_RESOURCES( SAMPLE_RC_SRCS ${SAMPLE_RCS} )
> QT4_WRAP_UI( SAMPLE_UI_HDRS ${SAMPLE_UIS} )
> QT4_WRAP_CPP( SAMPLE_MOC_SRCS ${SAMPLE_MOC_HDRS} )
>   
> ADD_EXECUTABLE(Spine ${SAMPLE_SRCS} ${SAMPLE_MOC_HDRS} ${SAMPLE_MOC_SRCS} ${SAMPLE_RC_SRCS} ${SAMPLE_UI_HDRS})
> 
> TARGET_LINK_LIBRARIES(Spine ${QT_LIBRARIES})
> TARGET_LINK_LIBRARIES(Spine ${ITK_LIBRARIES})
> TARGET_LINK_LIBRARIES(Spine ${VTK_LIBRARIES} QVTK)
> 
> On Tue, Jul 31, 2012 at 10:21 PM, jelemans <jelemans <at> macpacs.com> wrote:
> I'm just starting a QT +ITK project. Would you be willing to post your .pro
> file or an example to show how to get started?
> 
> Did you solve the problem?
> 
> TIA.
> 
> 
> 
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Including-ITK-in-QT-Creator-Project-ld-error-OSX-tp7409758p7580657.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> 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:
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> 
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> 
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> 
> Kitware offers ITK Training Courses, for more information visit:
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> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
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viateur Tuyisenge | 2 Aug 2012 11:42
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Quiver

Hello itk/vtk

Could you please tell me how I can visualize the optical flow fields 
like  I do in matlab with QUIVER()?

Thank you,

Regards

---
Viateur
 
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Willi Huber | 2 Aug 2012 11:57
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Re: Quiver

Hello Viateur,

I assume since this is more towards visualization you should use the VTK mailing list.

Good luck

Von: viateur Tuyisenge <viasenge-Qt13gs6zZMY@public.gmane.org>
An: "insight-users-RyaoCGfWeh4@public.gmane.org" <insight-users-RyaoCGfWeh4@public.gmane.org>
Gesendet: 11:42 Donnerstag, 2.August 2012
Betreff: [Insight-users] Quiver

Hello itk/vtk

Could you please tell me how I can visualize the optical flow fields 
like  I do in matlab with QUIVER()?

Thank you,

Regards

---
Viateur
 

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