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

[Matt McCormick]

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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>>
>