Background :
I mainly do medical image registration, and the gold standard mask in the data set is needed when training or testing the model. Some organizations provide RTstruct files, and I need to convert them to nii format for my convenience.
Method :
Use the dcmrtstruct2nii toolkit
Step 1 : Install the dcmrtstruct2nii package
pip install dcmrtstruct2nii
Step 2 : Use
Official website introduction:
Official website URL https://pypi.org/project/dcmrtstruct2nii/
# lets test it
from dcmrtstruct2nii import dcmrtstruct2nii, list_rt_structs
print(list_rt_structs('/path/to/dicom/rtstruct/file.dcm'))
dcmrtstruct2nii(rtstruct_file='/path/to/dicom/rtstruct/file.dcm',
dicom_file='/path/to/original/extracted/dicom/files',
output_path='/output/path')
Input
rtstruct_file=
the file path of the RTstruct file to be converted
dicom_file=
The folder path of the medical dicom image corresponding to the RTstruct
output_path=
Output folder path.
My attempts and results:
my python code:
from dcmrtstruct2nii import dcmrtstruct2nii, list_rt_structs
root='E:\Medical imaging dataset/'
patient_Data='patient_001/07-06-2012/'
print(list_rt_structs(root+patient_Data+'1.000000-BSCBLLLRSDCB-27748/1-1.dcm'))
dcmrtstruct2nii(rtstruct_file=root+patient_Data+'1.000000-BSCBLLLRSDCB-27748/1-1.dcm',
dicom_file=root+patient_Data+'201.000000-PANCREAS DI iDose 3-97846/',
output_path=root+patient_Data+'1.000000-BSCBLLLRSDCB-27748/')
"""
输出如下:
['Bowel_sm_CBCT', 'LUNG_L', 'LUNG_R', 'Stomach_duo_CBCT']
代表该RTstruct文件,包含四个mask
"""
In the end, output_path
5 nii files
image.nii are generated dicom_file=root+patient_Data+'201.000000-PANCREAS DI iDose 3-97846/'
by dicom in the folder.
mask_XX.nii rtstruct_file=root+patient_Data+'1.000000-BSCBLLLRSDCB-27748/1-1.dcm'
is generated from RTstruct file