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

[沈庄明]

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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