[英]How can I obtain 2D slices from a 3D NIfti volume?
I'm currently using the following code to convert DCM slices into NIfti images:我目前正在使用以下代码将 DCM 切片转换为 NIfti 图像:
import dicom2nifti
import os
dicom2nifti.convert_directory("input_path", "output_path", compression=True, reorient=True)
This code will generate a 3D NIfti volume.此代码将生成一个 3D NIfti 卷。
How can I obtain all the slices from this 3D NIfti volume?如何从这个 3D NIfti 卷中获取所有切片?
Use the package nibabel
.使用 package
nibabel
。 A simple working example opens your NIfTI file as a numpy 3D matrix, which can use for your processing needs:一个简单的工作示例将您的 NIfTI 文件打开为 numpy 3D 矩阵,可用于您的处理需求:
import nibabel as nib
import numpy as np
import matplotlib.plot as plt
my_nifti = nib.load('YOURNIFTIFILE.nii').get_fdata()
# get the shape of your NIfTI
my_nifti.shape
# access it as 3D numpy array
nifti_slice = my_nifti[:,:,59]
# display the slice
plt.imshow(nifti_slice)
plt.show()
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