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

[Dženan Zukić]

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 <https://issues.itk.org/jira/browse/ITK-3407>
> <https://issues.itk.org/jira/browse/ITK-3407?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel>
> 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
> <https://issues.itk.org/jira/browse/ITK-3407> 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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