[Insight-users] FW:
Luis Ibanez
luis.ibanez at kitware.com
Tue, 02 Mar 2004 17:53:09 -0500
Hi Raghu,
The problem seems to be with the arguments that you
are passing to the program. Right now you are using
the example in:
Insight/Examples/IO/
DicomSeriesReadImageWriter.cxx
This program expects as argument:
1) The directory where the DICOM files are
2) The filename of an output image file where the
set of image slices will be saved as a 3D dataset.
3) A *string identifying a dicom series*
You are passing:
F:\itk\data\MR\temp1\ 0
You are probably expecting the second argument "0"
to refer to the first series. That's not the case,
the program is taking "0" as the filename that you
want to use for saving the image data.
You sould be passing something like
F:\itk\data\MR\temp1 myOutputImageFile.mhd
The reason why the program is printing out all the
series Ids is for making it easier for you to take
one of those strings and use it as second argument
to the program. So, in a second run you can do
something more specific like:
DicomSeriesReaderImageWriter.exe
F:\itk\data\MR\temp1
myOutputImageFile.mhd
1.3.12.2.1107.5.1.4.24515.4.0.6770456214062487
(all in a single line...)
Where the last string "1.3.12.2...." is the identifier
of one of the series.
Once you save your DICOM data in a fileformat
such as Analyze of MetaImage, you will be ready
for start testing the ImageRegistration examples.
Deformable registration can easily take 40 minutes
if you are dealing with 3D datasets.
Did you use the Multi-Resolution framework ?
Regards,
Luis
----------------------
raghu venkatram wrote:
> Hello,
> I am using the dicom imageseriesreader, to read in a series of dicom
> images.
>
> My program arguments are:
> F:\itk\data\MR\temp1\ 0
>
> I only have one series in this directory, and nothing other than the
> dicom files
> are in this directory.
> Its reads through, gets the filenames in the series and gives an "abnormal
> program termination error". Debugging shows that the it crashes on the
> second
> file in the series. I would appreciate if anyone could help me out. also
> i see
> Chunyan had postes a similar problem.
>
> If i am able to read in a series of dicom images, i want to use one of the
> registration algorithms and pass the two series, I am not sure if this
> would
> give me 3d registration. I tried using the analyze format, with deformable
> registration, it takes close to 40 mins, which makes me think i am doing
> something wrong. I would be glad if somebody could help me sort things out.
>
>
> All my dicom images are viewable using the QT viewr, MRICro.
>
> Thanks in advance
> Raghu Venkatram
>
> /*=========================================================================
>
> Program: Insight Segmentation & Registration Toolkit
> Module: $RCSfile: DicomSeriesReadImageWrite.cxx,v $
> Language: C++
> Date: $Date: 2003/12/30 21:13:04 $
> Version: $Revision: 1.2 $
>
> Copyright (c) Insight Software Consortium. All rights reserved.
> See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
>
> This software is distributed WITHOUT ANY WARRANTY; without even
> the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
> PURPOSE. See the above copyright notices for more information.
>
> =========================================================================*/
>
> // Software Guide : BeginLatex
> //
> // This example illustrates how to read a DICOM series into a volume
> // and then save this volume in another file format.
> //
> // Software Guide : EndLatex
>
> /*=========================================================================
>
> Program: Insight Segmentation & Registration Toolkit
> Module: $RCSfile: itkDICOMImageSeriesTest.cxx,v $
> Language: C++
> Date: $Date: 2003/09/10 14:30:10 $xgoto-l
>
> Version: $Revision: 1.5 $
>
> Copyright (c) Insight Software Consortium. All rights reserved.
> See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
>
> This software is distributed WITHOUT ANY WARRANTY; without even
> the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
> PURPOSE. See the above copyright notices for more information.
>
> =========================================================================*/
> #if defined(_MSC_VER)
> #pragma warning ( disable : 4786 )
> #endif
> #include "itkDICOMImageIOFactory.h"
> #include "itkDICOMImageIO2.h"
> #include "itkImageSeriesReader.h"
> #include "itkDICOMSeriesFileNames.h"
> #include "itkAnalyzeImageIO.h"
> #include "itkImageFileWriter.h"
> #include
> "F:/itk/InsightToolkit-1.4.0/Testing/Code/BasicFilters/itkFilterWatcher.h"
>
> int main(int ac, char* av[])
> {
>
> typedef itk::AnalyzeImageIO ImageIOType;
>
> if(ac < 3)
> {
> std::cerr << "Usage: " << av[0] << " DicomDirectory
> ReverseOrder(0/1)\n";
> return EXIT_FAILURE;
> }
>
> typedef itk::Image<unsigned short,3> ImageNDType;
> typedef itk::Image<unsigned short,3> Image3DType;
> typedef itk::ImageSeriesReader<ImageNDType> ReaderType;
>
> itk::DICOMImageIO2::Pointer io = itk::DICOMImageIO2::New();
>
> // Get the DICOM filenames from the directory
> itk::DICOMSeriesFileNames::Pointer names =
> itk::DICOMSeriesFileNames::New();
> names->SetDirectory(av[1]);
>
> ReaderType::Pointer reader = ReaderType::New();
> reader->SetFileNames(names->GetFileNames());
> reader->SetImageIO(io);
> std::cout << names;
>
> FilterWatcher watcher(reader);
>
> try
> {
> if (atoi(av[2]))
> {
> reader->ReverseOrderOn();
> }
> reader->Update();
> reader->GetOutput()->Print(std::cout);
> }
> catch (itk::ExceptionObject &ex)
> {
> std::cout << ex;
> return EXIT_FAILURE;
> }
>
> /*
> typedef itk::ImageFileWriter< Image3DType > WriterType;
> WriterType::Pointer writer = WriterType::New();
>
> std::cout << "Writing the image as " << std::endl << std::endl;
> std::cout << av[2] << std::endl << std::endl;
>
> writer->SetFileName( "out.hdr" );
> ImageIOType::Pointer analyzeIO = ImageIOType::New();
> writer->SetImageIO(analyzeIO);
>
> writer->SetInput( reader->GetOutput() );
>
> try
> {
> writer->Update();
> }
> catch (itk::ExceptionObject &ex)
> {
> std::cout << ex;
> return EXIT_FAILURE;
> }
>
> */
>
>
> return EXIT_SUCCESS;
>
> }
>
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