Data for MICCAI #9

import torchio as tio

matrix_path, parcellation_path, mri_mni_path = _ # of a subject
mri_mni_skull_stripped_path = _
parcellation_mni_path = _

# Resample parcellation to MNI
matrix = tio.io.read_matrix(matrix_path)
parcellation = tio.LabelMap(parcellation_path, to_mni=matrix)
resample = tio.Resample(mri_mni_path, pre_affine_name='to_mni')
parcellation_mni = resample(parcellation)
parcellation_mni.save(parcellation_mni_path)

# Get brain mask
SMALLEST_BRAIN_LABEL = 24  # from colour table
extract_brain = tio.Lambda(lambda x: (x >= SMALLEST_BRAIN_LABEL))
brain_mask = extract_brain(parcellation_mni)

# Skull-stripping
def skull_strip(image, mask):
    image.data[~mask.data.bool()] = 0

mri = tio.ScalarImage(mri_mni_path)
skull_strip(mri, brain_mask)
mri.save(mri_mni_skull_stripped_path)