nibabel.get_data()
中的切片niimg出现问题。
使用Nipype教程的此功能时,
def plot_slice(fname, z_idx=5):
# Load the image and collect the data
# and orientation information
img = nib.load(fname)
data = img.get_data()
aff = img.get_affine()
# Find the center of the brain matrix
ctr = np.dot(np.linalg.inv(aff), [0, 0, 0, 1])[:3]
# Plot the data
vmin, vmax = (0, 1) if data.dtype == np.int16 else (30, 150)
plt.imshow(np.rot90(data[:, :, ctr[2] + z_idx]), cmap="gray", vmin=vmin, vmax=vmax)
plt.gca().set_axis_off()
运行
plot_slice("output/run001_bet.nii.gz")
然后结果证明是这样的;
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
<ipython-input-10-5b2c71c131be> in <module>()
----> 1 plot_slice("output/run001_bet.nii.gz")
<ipython-input-8-4c2563317c99> in plot_slice(fname, z_idx)
12 # Plot the data
13 vmin, vmax = (0, 1) if data.dtype == np.int16 else (30, 150)
---> 14 plt.imshow(np.rot90(data[:, :, ctr[2] + z_idx]),
15 cmap="gray", vmin=vmin, vmax=vmax)
16 plt.gca().set_axis_off()
IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices
因为ctr [2]由np.dot返回,所以它实际上是一个浮点数,即使它看起来像一个int。尝试int(ctr [2])+ z_idx。