medim_obj = MedImage.create_from_files(scan)
file_name = medim_obj.name.split("/")[-1]
image, brain_mask = medim_obj.compute_mask("{Brain}", "full", interp=True)
_, ventricle_mask = medim_obj.compute_mask("{Ventricles}", "full", interp=True)
_, brain_atlas = medim_obj.compute_mask("{BrainAtlas}", "full", interp=True)
_, ventricle_atlas = medim_obj.compute_mask("{VentriclesAtlas}", "full", interp=True)
raw_image = copy.deepcopy(image)
raw_image = helper.z_pad(raw_image)
raw_image = helper.xy_pad(raw_image)
image.data = helper.normalize(image.data, brain_mask.data)
image.data = helper.extract_brain(image.data, brain_mask.data)
skull_stripped = helper.z_pad(image)
skull_stripped = helper.xy_pad(skull_stripped)
ventricle_mask = helper.z_pad(ventricle_mask)
ventricle_mask = helper.xy_pad(ventricle_mask)
brain_mask = helper.z_pad(brain_mask)
brain_mask = helper.xy_pad(brain_mask)
ventricle_atlas = helper.z_pad(ventricle_atlas)
ventricle_atlas = helper.xy_pad(ventricle_atlas)
brain_atlas = helper.z_pad(brain_atlas)
brain_atlas = helper.xy_pad(brain_atlas)
image, brain_atlas = medim_obj.compute_mask("{Brain}",
"full",
interp=True)
_, ventricle_atlas = medim_obj.compute_mask("{Ventricles}",
"full",
interp=True)
raw_image = copy.deepcopy(image)
raw_image = helper.z_pad(raw_image)
raw_image = helper.xy_pad(raw_image)
np.save(
"/data/public/Segmentation_Dataset/MR_Dataset_Atlas/train/raw_images/{name}"
.format(name=file_name), raw_image.data)
image.data = helper.normalize(image.data, brain_atlas.data)
image.data = helper.extract_brain(image.data, brain_atlas.data)
skull_stripped = helper.z_pad(image)
skull_stripped = helper.xy_pad(skull_stripped)
np.save(
"/data/public/Segmentation_Dataset/MR_Dataset_Atlas/train/skull_stripped/{name}"
.format(name=file_name), skull_stripped.data)
ventricle_atlas = helper.z_pad(ventricle_atlas)
ventricle_atlas = helper.xy_pad(ventricle_atlas)
np.save(
"/data/public/Segmentation_Dataset/MR_Dataset_Atlas/train/ventricle_atlas/{name}"
.format(name=file_name), ventricle_atlas.data)
brain_atlas = helper.z_pad(brain_atlas)