[ITK] 答复: 转发: ITK try to read 4D dicom time series(3d, t), but get 3d*t

Fri Feb 26 14:02:43 EST 2016

Hey Cyril and Dženan,

Thanks very much for your help. I now fix this problem by using itkJoinSeriesImageFilter. This class could elevate a series of 3D volumes (x,y,z)*t into 4D level (x,y,z, t). Though I am not sure this is the best way for ITK to do so, at least it is the best solution I could find for now and hope this could help if anyone would work on 4D series using ITK in future. Here is part of my code:

typedef itk::JoinSeriesImageFilter<Image3DType, Image4DType> JoinSeriesImageFilterType;
typedef itk::GDCMSeriesFileNames NamesGeneratorType;
joinFilter = JoinSeriesImageFilterType::New();
NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
nameGenerator->AddSeriesRestriction("0008|0032");  //Use diffrent restriction depend on the dicom header
nameGenerator->SetUseSeriesDetails(true);
nameGenerator->SetDirectory(_filename);
typedef std::vector< std::string >   FileNamesContainer;
FileNamesContainer fileNames;
if (true == _isFileLoaded){
SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
for (seriesItr; seriesItr != seriesEnd; seriesItr++){
ReaderType::Pointer reader = ReaderType::New();
std::string seriesIdentifier = seriesItr->c_str();
fileNames = nameGenerator->GetFileNames(seriesIdentifier);
reader->SetFileNames(fileNames);
reader->Update();
joinFilter->SetInput(inputIndex, reader->GetOutput());
inputIndex++;
}
joinFilter->Update();

Best wishes,
Lifan
________________________________
发件人: Dženan Zukić [dzenanz at gmail.com]
发送时间: 2016年2月26日 9:47
收件人: Cyril Jaudet
抄送: Chen, Lifan; community at itk.org
主题: Re: [ITK] 转发: ITK try to read 4D dicom time series(3d, t), but get 3d*t

I only now see that you sent this only to me Cyril! I CC'd Lifan and the list.

On Thu, Feb 25, 2016 at 11:34 AM, Cyril Jaudet <drcjaudet at gmail.com<mailto:drcjaudet at gmail.com>> wrote:
Hi Lifan,
here some code that i past in the python interpreter of 3dslicer based on vtk.

_First download slicer and load multi image module.
_Import your serie with the dicom importer.
_Go into the multivolume support/multivolume explorer
_Enable frame copying or something similar.
Now you have two serie (module data to see/rename them)
1 multiframe serie
1 image that will be used as reference to extract the 3d + t image
_Copy/paste the following line in the python interpreter of 3dslicer.

from __main__ import vtk, qt, ctk, slicer
from math import *
import numpy as np
from vtk.util import numpy_support
import SimpleITK as sitk
import sitkUtils as su
import math

def convert4Dto3D(multi,reference):
    multiNode=slicer.util.getNode(multi)
    refNode=slicer.util.getNode(reference)
    multiImage=multiNode.GetImageData()
    N=multiNode.GetNumberOfFrames()
    for i in range (N):    #extract image
        im=vtk.vtkImageExtractComponents()
        im.SetInputData(multiImage)
        im.SetComponents(i)
        im.Update()
        frame=slicer.modules.volumes.logic().CloneVolume(slicer.mrmlScene,refNode,'frame_'+str(i))
        frame.SetAndObserveImageData(im.GetOutput())

_then type:
convert4Dto3D(multi,reference)
changing the name of multi and reference by the corresponding name of your data
_it will extract the image under the name frame0, frame1...
_save them

Hope that help,

Cyril Jaudet
UZBrussel

2016-02-24 18:46 GMT+01:00 Dženan Zukić <dzenanz at gmail.com<mailto:dzenanz at gmail.com>>:
Hi Lifan,

did you examine the DICOM headers? Do different timepoints have different acquisition times?

Regards,
Dženan

On Wed, Feb 24, 2016 at 11:22 AM, Chen, Lifan <LCHEN41 at mgh.harvard.edu<mailto:LCHEN41 at mgh.harvard.edu>> wrote:
Hey all,

Any help would be appreciated. This problem really gets me in for couple of days.

Thanks,
Lifan
________________________________
发件人: Chen, Lifan
发送时间: 2016年2月23日 17:48
收件人: community at itk.org<mailto:community at itk.org>
主题: ITK try to read 4D dicom time series(3d, t), but get 3d*t

Hi all,

These days, I am trying to use ITK to handle 4D dicom series (3d+t). I use GDCMSeriesFileNames to generate seriesUIDs and ImageSeriesReader to read these images.

The following is part of my code:
typedef double    PixelType;
typedef itk::Image< PixelType, 4>         Image4DType;                  //4D image type
typedef itk::Image< PixelType, 3>         Image3DType;                  //3D image type
typedef itk::ImageSeriesReader< Image4DType >        ReaderType;
typedef itk::GDCMImageIO       ImageIOType;
reader = ReaderType::New();
dicomIO = ImageIOType::New();
typedef itk::GDCMSeriesFileNames NamesGeneratorType;
NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
nameGenerator->AddSeriesRestriction("0008|0021");
nameGenerator->SetUseSeriesDetails(true);
nameGenerator->SetDirectory(_filename);
typedef std::vector< std::string >    SeriesIdContainer;
const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
_isFileLoaded = !(seriesUID.empty());
if (true == _isFileLoaded){
SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
std::string seriesIdentifier = seriesUID.begin()->c_str();
typedef std::vector< std::string >   FileNamesContainer;
FileNamesContainer fileNames;
fileNames = nameGenerator->GetFileNames(seriesIdentifier);
reader->SetFileNames(fileNames);
reader->SetImageIO(dicomIO);
reader->Update();
}

I have tried this code and the reader worked well. However I got a [x,y,z*t, 1] data, but not [x, y, z, t] data. I understand the problem may caused by nameGenerator, but I use SetUseSeriesDetails and AddSeriesRestriction("0008|0021")(aquisition time)which are implied by documents to handle 4d images.I have also tried several methods but all not work. I wonder whether ITK have an original method to handle 4d images.

Have anyone ever met this problem before? Any help or recommendations would be appreciated.

Thanks,
Lifan

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