[ITK-users] Strange situation when ITK writes DICOM file

[沈庄明]

Hi Matt,

Thank you for your reply.  I have tried to use ITK Git master and the code provided by Dženan, it can work correctly. Thanks again.

By the way, could you list what data types (e.g. char type) do the updated GDCM support now?


Regards,

Zhuangming Shen 
________________________________________
From: Matt McCormick <matt.mccormick at kitware.com>
Sent: Thursday, May 5, 2016 10:21 PM
To: 沈庄明
Cc: Dženan Zukić; insight-users at itk.org
Subject: Re: [ITK-users] Strange situation when ITK writes DICOM file

Hi Zhuangming Shen,

GDCM was updated in ITK Git master, to be released in ITK 4.10.
Instructions on how to obtain this version can be found here:

  https://itk.org/Wiki/ITK/Git/Download

Thanks,
Matt

On Mon, May 2, 2016 at 10:40 PM, 沈庄明 <zhuangming.shen at sphic.org.cn> wrote:
> Hi Dženan,
>
>
> Thanks for your prompt response. I used ITK 4.9.1 and your attached code
> (just changed inDir and outFile) to test both public DICOM data
> (http://www.osirix-viewer.com/datasets/DATA/BREBIX.zip) and private DICOM
> data, the results are still incorrect (please see the attached screenshot).
> What's the problem?
>
>
> Besides, as far as I know, rescaling the intensity from short type to char
> type leads to lose precision because the DICOM tags ( (0028,0100) and
> (0028,0101) ) show the BitsAllocated is 16-bits and the BitsStored is
> 12-bits. Consequently, this solution doesn't seem to be a good solution. Is
> it possible to output the DICOM file by other tools (e.g. DCMTK) if the GDCM
> doesn't support short type?
>
>
>
> Regards,
>
>
> Zhuangming Shen
>
>
>
>
> ________________________________
> From: Dženan Zukić <dzenanz at gmail.com>
> Sent: Friday, April 29, 2016 9:59 PM
> To: 沈庄明
> Cc: insight-users at itk.org; Matt McCormick
>
> Subject: Re: [ITK-users] Strange situation when ITK writes DICOM file
>
> Hi Shen,
>
> GDCM version was updated recently. It now complains that short type is
> unsupported, and works correctly with char type. I attached an example which
> rescales the intensity and works correctly.
>
> Regards,
> Dženan
>
> On Fri, Apr 29, 2016 at 3:17 AM, 沈庄明 <zhuangming.shen at sphic.org.cn> wrote:
>>
>> Hi Dženan,
>>
>>
>> I'd like to know if the bug regarding 3D DICOM writer has been fixed. When
>> I tried to run the same code but using ITK 4.9.1, I still got the same
>> results, i.e. the output DICOM file does not properly record original
>> image's origin and spacing.
>>
>>
>>
>> Regards,
>>
>>
>> Zhuangming Shen
>>
>> ________________________________
>> From: Dženan Zukić <dzenanz at gmail.com>
>> Sent: Saturday, December 26, 2015 1:44 AM
>> To: 沈庄明
>> Cc: insight-users at itk.org
>> Subject: Re: [ITK-users] Strange situation when ITK writes DICOM file
>>
>> I have confirmed this bug and entered it into tracker along with a DICOM
>> series which reproduces it.
>>
>> Thanks Shen
>>
>> On Tue, Dec 22, 2015 at 8:41 PM, 沈庄明 <zhuangming.shen at sphic.org.cn> wrote:
>>>
>>> Hi all,
>>>
>>>
>>> I met a very strange situation when I used ITK 4.8.1. I'd like to read a
>>> DICOM series, write it to a DICOM file (i.e. save the volume created by the
>>> DICOM series to a .dcm file), and read the DICOM file. Theoretically, the
>>> DICOM series and the DCM file should have the same information, e.g origin,
>>> spacing, size. However, My results show me that the information has been
>>> changed. When I use other ITK-support file format (e.g. nii, nrrd), the
>>> information has not been changed. It seems a bug. My code and results are
>>> listed as below. Has anyone met the same situation?
>>>
>>>
>>> Regards,
>>>
>>>
>>> Zhuangming Shen
>>>
>>>
>>>
>>>
>>> ================   My code  =================
>>>
>>>
>>> import itk
>>>
>>> input_dir = "/home/zshen/workspace/Data/testDCM/bbb"
>>> output_filename = "/home/zshen/workspace/Data/bbb2.dcm"
>>>
>>> # read DICOM series
>>> dicom_io = itk.GDCMImageIO.New()
>>>
>>> reader = itk.ImageSeriesReader[itk.Image.SS3].New()
>>> reader.SetImageIO(dicom_io)
>>>
>>> name_generator = itk.GDCMSeriesFileNames.New()
>>> name_generator.SetUseSeriesDetails(True)
>>> name_generator.SetDirectory(input_dir)
>>>
>>> series_uid = name_generator.GetSeriesUIDs()
>>>
>>> series_identifier = series_uid[0]
>>>
>>> file_names = name_generator.GetFileNames(series_identifier)
>>>
>>> reader.SetFileNames(file_names)
>>> reader.Update()
>>>
>>> print("****  series DICOM information: *****")
>>> print("size:
>>> "+str(reader.GetOutput().GetLargestPossibleRegion().GetSize()))
>>> print("origin: "+str(reader.GetOutput().GetOrigin()))
>>> print("spacing: "+str(reader.GetOutput().GetSpacing()))
>>>
>>> writer = itk.ImageFileWriter[itk.Image.SS3].New()
>>> writer.SetInput(reader.GetOutput())
>>> writer.SetFileName(output_filename)
>>> writer.Update()
>>>
>>> # read again
>>> reader2 = itk.ImageFileReader[itk.Image.SS3].New()
>>> reader2.SetFileName(output_filename)
>>> reader2.Update()
>>>
>>> print("****  DICOM information: *****")
>>> print("size:
>>> "+str(reader2.GetOutput().GetLargestPossibleRegion().GetSize()))
>>> print("origin: "+str(reader2.GetOutput().GetOrigin()))
>>> print("spacing: "+str(reader2.GetOutput().GetSpacing()))
>>>
>>>
>>> =================  My results ====================
>>>
>>> ****  series DICOM information: *****
>>> size: itkSize3 ([512, 512, 118])
>>> origin: itkPointD3 ([-229.5, -96.5, -553])
>>> spacing: itkVectorD3 ([0.896484, 0.896484, 3])
>>> ****  DICOM information: *****
>>> size: itkSize3 ([512, 512, 118])
>>> origin: itkPointD3 ([0, 0, 0])
>>> spacing: itkVectorD3 ([0.896484, 0.896484, 1])
>>>
>>>
>>>
>>>
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>>
>