How to extract 2D patches from 3D medical image

vision
2

Hi @Surbhi_Khushu,

You can achieve that using TorchIO:

from pathlib import Path
import torchio as tio

out_dir = Path('/tmp/patches')
out_dir.mkdir(exist_ok=True)

patch_size = 64
patch_overlap = 18

subject = tio.Subject(
    ct=tio.Image('/tmp/ct.nii.gz', type=tio.INTENSITY),
    mr=tio.Image('/tmp/mr.nii.gz', type=tio.INTENSITY),
)

sampler = tio.data.GridSampler(
    subject,
    patch_size,
    patch_overlap,
)

for i, patch in enumerate(sampler):
    patch.ct.save(out_dir / f'ct_{i}.nii.gz')
    patch.mr.save(out_dir / f'mr_{i}.nii.gz')

Full volumes:

Screenshot
Screenshot1410×1298 211 KB

One of the extracted patches:

Screenshot
Screenshot1398×1298 162 KB

Take a look at the documentation for patch-based pipelines.