python医学影像2Ddicom文件转成3Dnii文件(保留原始dicom信息)

最近处理医院影像数据时,遇到的需求:把预处理后的MRI影像的每个序列的所有dicom文件保存成nii文件,并且要保留原始的dicom信息

预处理后的MRI影像序列

image.png

每个序列下有多张dicom文件

image.png

Python代码:把每个序列的所有dicom文件保存成nii文件,并保留原始的tag信息

导入需要的包

#edited by NickYu 2020.10.23
import numpy as np
import SimpleITK as sitk
import pydicom 
import h5py
import os
import nibabel as nib
import dicom2nifti

定义函数

def dicom2Nii(folderPath,savefolder):
    '''
    dicom序列转成3维的nii文件，并保留原始的dicom元数据信息
    '''
    count_study = 0
    for every_study in os.listdir(folderPath):#遍历所有的病历号
        count_study +=1
        tmp_MR_path = os.path.join(folderPath,every_study,'MR')#DWI ,T2等
        _save_path =os.path.join(savefolder,every_study,'MR2Nii')
        for every_MRI in os.listdir(tmp_MR_path):#每个病历号下面可能有多次MRI
            tmp_MRI_path = os.path.join(tmp_MR_path,every_MRI)
            tmp_save_path = os.path.join(_save_path,every_MRI)
            if not os.path.exists(tmp_save_path):
                os.makedirs(tmp_save_path)
            all_Series_path = os.listdir(tmp_MRI_path)
            #print(all_Series_path) #['DCE00001', 'DCE00002', 'DCE00003', 'DCE00004', 'DCE00005', 'DCE00006']
            for every_DCE_series in  all_Series_path:
                #print(every_DCE_series) # DCE00001
                all_dicoms = os.path.join(tmp_MRI_path,every_DCE_series)
                
                #print(all_dicoms)
                # path_read:读取dicom的文件路径  path_save:保存nii的文件路径
                def dcm2nii(path_read, path_save):# from CSDN;function: transfer dcm_series into nii file
                    # GetGDCMSeriesIDs读取序列号相同的dcm文件
                    series_id = sitk.ImageSeriesReader.GetGDCMSeriesIDs(path_read)
                    # GetGDCMSeriesFileNames读取序列号相同dcm文件的路径，series[0]代表第一个序列号对应的文件
                    series_file_names = sitk.ImageSeriesReader.GetGDCMSeriesFileNames(path_read, series_id[0])
                    #print(len(series_file_names))  #11
                    series_reader = sitk.ImageSeriesReader()
                    series_reader.SetFileNames(series_file_names)
                    image3d = series_reader.Execute()
                    sitk.WriteImage(image3d, path_save)
                path_save = tmp_save_path + "\\"+every_DCE_series+".nii"
                if os.path.exists(path_save):
                    continue
                dcm2nii(all_dicoms, path_save) #调用函数执行

定义待读取文件夹路径和nii文件存储路径

if __name__ =="__main__":
    folderPath =r"G:\cut_SkinData_Copy\Cut_Skin"
    savefolder = r"G:\2020.10.cut_Skin_DATA(nii)"
    dicom2Nii(folderPath,savefolder)

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