[Insight-users] Errors while reading DICOM time series (4D) using DicomSeriesReadImageWrite2

[Luis Ibanez]

Hi Martin,


Thanks for your detailed message.



1) The order of the parameters in DicomSeriesReadImageWrite2
    seem to be correct. The are:

           1. Directory where your dicom files are
           2. Filename of the image to be used as output
           3. Series ID of the DICOM image to read

    Could you please give use more details on how you arrived
    to the conclusion that parameters (2) and (3) were swapped ?




2) It is not surprising that the reader have problems loading
    your 4D dataset.  The message about slices having repeated
    positions is to be expected, because, presumably the acquisition
    protocol is such that for every position in the table, your
    scanner acquired N time points.

    The DICOM filename generator goes through the list of files
    in the directory and sort them out based on the table position.
    Given that you have the N timepoints, the sorting algorithm
    will find N image with the same table position.

    Please read the following message
    sent to the list on May 2004:

     http://www.itk.org/pipermail/insight-users/2004-May/008674.html


     You probably should contact sachin and kindly request from him
     his Dicom File generation class.

     It would be great if Sachin find interesting to write a short
     paper to the Insight Journal, describing the use of his new
     class, and contributing the code.  In this way, we could include
     his class in a future release of ITK.





3)  Also, please note that if you want to load a time series,
     you should instantiate your image as a 4D image. See details
     on the following message.

     http://www.itk.org/pipermail/insight-users/2004-May/008702.html





4)  Remember that you can search the archives of the users list
     with Google by using the following link:

http://www.google.com/advanced_search?as_sitesearch=www.itk.org&as_epq=insight%2Dusers






Regards,



     Luis



---------------------
Martin Kavec wrote:
> Hi fellows,
> 
> I have a DICOM time series (4D image) acquires on a recent Philips MRI, which 
> I would like to further process with ITK-2.4.1. After reading the ITK 
> Software Guide, I compiled DicomSeriesReadImageWrite2 (on linux) and tried to 
> use it, but there are few issues:
> 
> 1. a minor one, usage says
>  Usage:
> ./DicomSeriesReadImageWrite2 DicomDirectory  outputFileName  [seriesName]
> but the arguments have to be passed the other way around, the seriesName 
> followed by the  outputFileName :)
> 
> 2. running the program outputs lots of errors such as:
> Error: In /opt/ITK-2.4.1/Utilities/gdcm/src/gdcmSerieHelper.cxx, line 345, 
> function bool 
> gdcm::SerieHelper::ImagePositionPatientOrdering(gdcm::GdcmFileList*)
> File: fMRI_GE/TEST_B0_MAP.fMRI_GE_hos_SENSE.20050713.img0463 Distance: 47.281 
> position is not unique
> 
> 3. ITK-2.4.1 reads in the image as 
> ImageRegion (0x80e5c98)
>   Dimension: 4
>   Index: [0, 0, 0, 0]
>   Size: [80, 80, 480, 1]
> 
> instead of
> 
>   Size: [80, 80, 24, 20]
> 
> that is the number of slices and time points is incorrect. To get this 
> information I used:
> 
> std::cout << reader->GetOutput()->GetLargestPossibleRegion() << std::endl;
> 
> Should I file a bug report?
> 
> Cheers,
> 
> Martin
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