[英]how to slice 3d Nifti(.nii) image to 2d image with particular plane?
我正在编写一个脚本,可以估计 3d Nifti(.nii) 图像的清晰度。 在我的方法中,我需要取出 3d 图像的 xz(axis) 切片,然后将其保存为 .png 文件。(为了效率,只取一个)然后,估计图像的清晰度。 但是,我不知道如何使用特定平面(切片)对 3d 图像进行切片。 是否有任何现有的代码或库可以进行切片?
我正在使用 Python 3.7(在 Window 10 中运行)。
我试过这个库: https : //pypi.org/project/nii2png/但是,它不能输出一个硅片。
我也试过这个页面的方法https://nipy.org/nibabel/coordinate_systems.html#introducing-someone但是,它不起作用。 原因可能是 Nifti 文件不同。 我认为有两种 nifti 格式的文件。
import nibabel as nib
import numpy as np
import matplotlib.pyplot as plt
def show_slices(slices):
""" Function to display row of image slices """
fig, axes = plt.subplots(1, len(slices))
for i, slice in enumerate(slices):
axes[i].imshow(slice.T, cmap="gray", origin="lower")
data = nib.load('D:\\Work\\Script\\__Project\\s\\ADNI\\good_img\\MPRAGE_SENSE2\\2012-11-08_07_32_36.0\\S174286\\ADNI_002_S_5018_MR_MPRAGE_SENSE2__br_raw_20121112145413785_28_S174286_I346236.nii')
data.get_fdata()
data = data.get_fdata()
data.shape
#d_data = np.delete(data, 3, 0) #doesn't work, because it's object of type 'Nifti1Image'
#matplotlib inline
#plt.imshow(data.get_data()[:,:,50])
plt.plot(np.mean(data,axis=(0,1,2)))
plt.show()
slice_0 = data[26, :, :, :]
slice_1 = data[:, 30, :, :]
slice_2 = data[:, :, 16, :]
slice_3 = data[:, :, :, 0]
show_slices([slice_0, slice_1, slice_2, slice_3])
plt.suptitle("Center slices for EPI image")
然后我得到了错误:
Warning (from warnings module):
File "D:\Program_Files_2\Python\lib\site-packages\dicom\__init__.py", line 53
warnings.warn(msg)
UserWarning:
This code is using an older version of pydicom, which is no longer
maintained as of Jan 2017. You can access the new pydicom features and API
by installing `pydicom` from PyPI.
See 'Transitioning to pydicom 1.x' section at pydicom.readthedocs.org
for more information.
Traceback (most recent call last):
File "D:\Work\Script\__Project\s\try_load_nii_image_and_view_slice_3.py", line 25, in <module>
show_slices([slice_0, slice_1, slice_2, slice_3])
File "D:\Work\Script\__Project\s\try_load_nii_image_and_view_slice_3.py", line 9, in show_slices
axes[i].imshow(slice.T, cmap="gray", origin="lower")
File "D:\Program_Files_2\Python\lib\site-packages\matplotlib\__init__.py", line 1601, in inner
return func(ax, *map(sanitize_sequence, args), **kwargs)
File "D:\Program_Files_2\Python\lib\site-packages\matplotlib\cbook\deprecation.py", line 369, in wrapper
return func(*args, **kwargs)
File "D:\Program_Files_2\Python\lib\site-packages\matplotlib\cbook\deprecation.py", line 369, in wrapper
return func(*args, **kwargs)
File "D:\Program_Files_2\Python\lib\site-packages\matplotlib\axes\_axes.py", line 5671, in imshow
im.set_data(X)
File "D:\Program_Files_2\Python\lib\site-packages\matplotlib\image.py", line 690, in set_data
.format(self._A.shape))
TypeError: Invalid shape (1, 256, 256) for image data
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