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

[Dženan Zukić]

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> 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>:
>
>> 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>
>> 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
>>> *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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