使用dicom2nifti无法正常工作的转换

Question

我有一系列的dicom文件(.dcm)给我想要转换成nii.gz文件的每个病人，但是在下面的转换中没有发生任何事情(甚至错误信息).

import dicom2nifti
dicom2nifti.settings.set_gdcmconv_path('C:/Program Files/GDCM 3.0/bin/gdcmconv.exe')
dicom2nifti.convert_directory('M0_1', 'M0_1.nii.gz')

此错误发生在尝试其他方法时..。

import dicom2nifti
dicom2nifti.settings.set_gdcmconv_path('C:/Program Files/GDCM 3.0/bin/gdcmconv.exe')
dicom2nifti.dicom_series_to_nifti('M0_1', 'M0_1.nii.gz')

错误日志：

Traceback (most recent call last):
  File ".\test.py", line 5, in <module>
    dicom2nifti.dicom_series_to_nifti('M0_1', 'M0_1.nii.gz')
  File "D:\Anaconda3\envs\pydicom\lib\site-packages\dicom2nifti\convert_dicom.py", line 78, in dicom_series_to_nifti
    return dicom_array_to_nifti(dicom_input, output_file, reorient_nifti)
  File "D:\Anaconda3\envs\pydicom\lib\site-packages\dicom2nifti\convert_dicom.py", line 112, in dicom_array_to_nifti
    if not are_imaging_dicoms(dicom_list):
  File "D:\Anaconda3\envs\pydicom\lib\site-packages\dicom2nifti\convert_dicom.py", line 151, in are_imaging_dicoms
    if common.is_philips(dicom_input):
  File "D:\Anaconda3\envs\pydicom\lib\site-packages\dicom2nifti\common.py", line 102, in is_philips
    header = dicom_input[0]
IndexError: list index out of range

档案结构：

M0_1
   |----IM-0001-0001.dcm
   |----IM-0001-0002.dcm
   ........
   |----IM-0001-000299.dcm
   |----IM-0001-000300.dcm

环境: windows10，python: 3.6，dicom2nifti2.3.0

我哪里做错了？

或者还有其他方法来转化它呢？

提前感谢！

Answer 1

我没有使用dicom2nifti，但是您可以使用SimpleITK将DICOM转换为Nifti。

下面是应该完成这项工作的代码：

import SimpleITK as sitk

reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames('M0_1')
reader.SetFileNames(dicom_names)
image = reader.Execute()

# Added a call to PermuteAxes to change the axes of the data
image = sitk.PermuteAxes(image, [2, 1, 0])

sitk.WriteImage(image, 'M0_1.nii.gz')

您可以在这里了解更多关于SimpleITK的信息：https://simpleitk.readthedocs.io/

更新:我向SimpleITK的PermuteAxes添加了一个调用，将轴顺序从X.更改为Z。