Is there a convenient way to plot a slice from a patient volume?

Is there any convenient way to display for example nth-slice of subject image of subjects_dataset[0] ?

I want to visualize slices as I apply tranforms to them, the only thing I came up with is converting the the 3D Tensor back to .nii image and from that plotting the slice.

Can you suggest any convenient method ?

Thankyou and much appreciated.

Faraz

[fepegar]

It depends on what plane you want to visualize. You can just plot data[..., n_slice]. Here’s some code that might be helpful:

https://github.com/fepegar/miccai-educational-challenge-2019/blob/94067cdb99830ea21e51964ac9c20a34c28aaea4/visualization.py#L113-L173

It will look like this:

[fepegar]

You just need to slice your 3D volume along the third axis, which is the one that goes from inferior (slice 0) to superior (slice 55), if your image is RAS.

size_r, size_a, size_s = data.shape
for k in range(size_s):
    slice = data[:, :, k]. # or just data[..., k]
    plt.imshow(slice)
    plt.show()