def smoothness_loss(true_y, pred_y):
y0 = tf.reshape(pred_y[:, :, :, :, 0],
[tf.shape(pred_y)[0], *K.int_shape(pred_y)[1:4], 1])
y1 = tf.reshape(pred_y[:, :, :, :, 1],
[tf.shape(pred_y)[0], *K.int_shape(pred_y)[1:4], 1])
y2 = tf.reshape(pred_y[:, :, :, :, 2],
[tf.shape(pred_y)[0], *K.int_shape(pred_y)[1:4], 1])
dx = tf.abs(volumeGradients(y0))
dy = tf.abs(volumeGradients(y1))
dz = tf.abs(volumeGradients(y2))
norm = functools.reduce(lambda x, y: x * y,
K.int_shape(pred_y)[1:5]) * batch_size
return tf.reduce_sum((dx + dy + dz) / norm, axis=[1, 2, 3, 4])
def volumeGradients(tf_vf):
# batch_size, xaxis, yaxis, zaxis, depth = \
shapes = (tf.shape(tf_vf)[0], *K.int_shape(tf_vf)[1:])
dx = tf_vf[:, 1:, :, :, :] - tf_vf[:, :-1, :, :, :]
dy = tf_vf[:, :, 1:, :, :] - tf_vf[:, :, :-1, :, :]
dz = tf_vf[:, :, :, 1:, :] - tf_vf[:, :, :, :-1, :]
# Return tensors with same size as original image by concatenating
# zeros. Place the gradient [I(x+1,y) - I(x,y)] on the base pixel (x, y).
shape = tf.stack([shapes[0], 1, shapes[2], shapes[3], shapes[4]])
dx = array_ops.concat([dx, tf.zeros(shape, tf_vf.dtype)], 1)
dx = array_ops.reshape(dx, tf.shape(tf_vf))
# shape = tf.stack([batch_size, xaxis, 1, zaxis, depth])
shape = tf.stack([shapes[0], shapes[1], 1, shapes[3], shapes[4]])
dy = array_ops.concat([dy, array_ops.zeros(shape, tf_vf.dtype)], 2)
dy = array_ops.reshape(dy, tf.shape(tf_vf))
# shape = tf.stack([batch_size, xaxis, yaxis, 1, depth])
shape = tf.stack([shapes[0], shapes[1], shapes[2], 1, shapes[4]])
dz = array_ops.concat([dz, array_ops.zeros(shape, tf_vf.dtype)], 3)
dz = array_ops.reshape(dz, tf.shape(tf_vf))
return tf.reshape(array_ops.stack([dx, dy, dz], 4),
[shapes[0], shapes[1], shapes[2], shapes[3], 3])
def invertDisplacements(args):
x, y, z = K.int_shape(args)[1:4]
disp = args
# ij indexing doesn't change (x,y,z) to (y,x,z)
grid = tf.expand_dims(
tf.stack(
tf.meshgrid(tf.linspace(0., x - 1., x),
tf.linspace(0., y - 1., y),
tf.linspace(0., z - 1., z),
indexing='ij'), -1), 0)
# replicate along batch size
stacked_grids = tf.tile(grid, (tf.shape(args)[0], 1, 1, 1, 1))
print(stacked_grids.shape)
grids = [tf.expand_dims(stacked_grids[:, :, :, :, i], 4) for i in range(3)]
print(grids[0].shape)
displaced_grids = [remap3d(subgrid, disp) for subgrid in grids]
print(displaced_grids[0].shape)
inverted_grids = [g - disp_g for g, disp_g in zip(grids, displaced_grids)]
print(inverted_grids[0].shape)
inverted_grid = tf.stack(
[tf.squeeze(inverted_grids[i], 4) for i in range(3)], 4)
print(inverted_grid.shape)
return inverted_grid
def avg_batch_mse_loss_exaustive(y_true, y_pred):
batch_size = K.int_shape(y_pred)[0]
loss = 0
N = 0
for i in range(0, batch_size):
for j in range(i + 1, batch_size):
loss += mean_squared_error(y_pred[i], y_pred[j])
N += 1
loss /= N
def smoothness_loss(true_y, pred_y):
dx = tf.abs(volumeGradients(tf.expand_dims(pred_y[:, :, :, :, 0], -1)))
dy = tf.abs(volumeGradients(tf.expand_dims(pred_y[:, :, :, :, 1], -1)))
dz = tf.abs(volumeGradients(tf.expand_dims(pred_y[:, :, :, :, 2], -1)))
return tf.reduce_sum(
(dx + dy + dz) /
(functools.reduce(lambda x, y: x * y,
K.int_shape(pred_y)[1:5]) * batch_size),
axis=[1, 2, 3, 4])
def sampling(args):
z_mean = args[0]
z_log_sigma = args[1]
batch = K.shape(z_mean)[0]
dim = K.int_shape(z_mean)[1]
#flattened_dim = functools.reduce(lambda x,y:x*y,[*dim,3])
epsilon = tf.reshape(K.random_normal(shape=(batch, dim), dtype=tf.float32),
(batch, dim))
xout = z_mean + K.exp(z_log_sigma) * epsilon
return xout
def sampling(args):
"""Reparameterization trick by sampling fr an isotropic unit Gaussian.
# Arguments
args (tensor): mean and log of variance of Q(z|X)
# Returns
z (tensor): sampled latent vector
"""
z_mean, z_log_var = args
batch = K.shape(z_mean)[0]
dim = K.int_shape(z_mean)[1]
# by default, random_normal has mean=0 and std=1.0
epsilon = K.random_normal(shape=(batch, dim))
return z_mean + K.exp(0.5 * z_log_var) * epsilon
def get_output_shape_for(self, input_shape):
if self._output_shape is None:
# if TensorFlow, we can infer the output shape directly:
if K._BACKEND == 'tensorflow':
if type(input_shape) is list:
xs = [K.placeholder(shape=shape) for shape in input_shape]
x = self.call(xs)
else:
x = K.placeholder(shape=input_shape)
x = self.call(x)
if type(x) is list:
return [K.int_shape(x_elem) for x_elem in x]
else:
return K.int_shape(x)
# otherwise, we default to the input shape
return input_shape
elif type(self._output_shape) in {tuple, list}:
nb_samples = input_shape[0] if input_shape else None
return (nb_samples, ) + tuple(self._output_shape)
else:
shape = self._output_shape(input_shape)
if type(shape) not in {list, tuple}:
raise Exception('output_shape function must return a tuple')
return tuple(shape)
def _time_distributed_dense(x,
w,
b=None,
dropout=None,
input_dim=None,
output_dim=None,
timesteps=None,
training=None):
"""Apply `y . w + b` for every temporal slice y of x.
# Arguments
x: input tensor.
w: weight matrix.
b: optional bias vector.
dropout: wether to apply dropout (same dropout mask
for every temporal slice of the input).
input_dim: integer; optional dimensionality of the input.
output_dim: integer; optional dimensionality of the output.
timesteps: integer; optional number of timesteps.
training: training phase tensor or boolean.
# Returns
Output tensor.
"""
if not input_dim:
input_dim = K.shape(x)[2]
if not timesteps:
timesteps = K.shape(x)[1]
if not output_dim:
output_dim = K.int_shape(w)[1]
if dropout is not None and 0. < dropout < 1.:
# apply the same dropout pattern at every timestep
ones = K.ones_like(K.reshape(x[:, 0, :], (-1, input_dim)))
dropout_matrix = K.dropout(ones, dropout)
expanded_dropout_matrix = K.repeat(dropout_matrix, timesteps)
x = K.in_train_phase(x * expanded_dropout_matrix, x, training=training)
# collapse time dimension and batch dimension together
x = K.reshape(x, (-1, input_dim))
x = K.dot(x, w)
if b is not None:
x = K.bias_add(x, b)
# reshape to 3D tensor
if K.backend() == 'tensorflow':
x = K.reshape(x, K.stack([-1, timesteps, output_dim]))
x.set_shape([None, None, output_dim])
else:
x = K.reshape(x, (-1, timesteps, output_dim))
return x
def exponentialMap(args):
grads = args
x, y, z = K.int_shape(args)[1:4]
# ij indexing doesn't change (x,y,z) to (y,x,z)
grid = tf.expand_dims(
tf.stack(
tf.meshgrid(tf.linspace(0., x - 1., x),
tf.linspace(0., y - 1., y),
tf.linspace(0., z - 1., z),
indexing='ij'), -1), 0)
# replicate along batch size
stacked_grids = tf.tile(grid, (tf.shape(grads)[0], 1, 1, 1, 1))
res = tfVectorFieldExp(grads, stacked_grids, n_steps=steps)
return res
def tfVectorFieldExp(grad, grid, n_steps):
N = n_steps
shapes = tf.shape(grad)
batch_size, size_x, size_y, size_z, channels = shapes[0], *K.int_shape(
grad)[1:5]
id_x = tf.reshape(grid[:, :, :, :, 0],
[batch_size, size_x, size_y, size_z, 1])
id_y = tf.reshape(grid[:, :, :, :, 1],
[batch_size, size_x, size_y, size_z, 1])
id_z = tf.reshape(grid[:, :, :, :, 2],
[batch_size, size_x, size_y, size_z, 1])
ux = grad[:, :, :, :, 0]
uy = grad[:, :, :, :, 1]
uz = grad[:, :, :, :, 2]
dvx = ux / (2.0**N)
dvy = uy / (2.0**N)
dvz = uz / (2.0**N)
dvx = id_x + tf.reshape(dvx, [batch_size, size_x, size_y, size_z, 1])
dvy = id_y + tf.reshape(dvy, [batch_size, size_x, size_y, size_z, 1])
dvz = id_z + tf.reshape(dvz, [batch_size, size_x, size_y, size_z, 1])
for n in range(0, N - 1):
cache_tf = tf.stack([dvx - id_x, dvy - id_y, dvz - id_z], 4)
cache_tf = tf.reshape(cache_tf,
[batch_size, size_x, size_y, size_z, 3])
dvx = remap3d(dvx, cache_tf) + tf.expand_dims(cache_tf[:, :, :, :, 0],
-1)
dvy = remap3d(dvy, cache_tf) + tf.expand_dims(cache_tf[:, :, :, :, 1],
-1)
dvz = remap3d(dvz, cache_tf) + tf.expand_dims(cache_tf[:, :, :, :, 2],
-1)
ox = dvx - id_x
oy = dvy - id_y
oz = dvz - id_z
out = tf.reshape(tf.stack([ox, oy, oz], 4),
[batch_size, size_x, size_y, size_z, 3])
return out
def _bottleneck(inputs: "Layer",
filters: int,
kernel: int or Tuple[int, int],
expansion_factor: int,
strides: int or Tuple[int, int],
residuals: bool = False) -> "Layer":
"""Bottleneck
This function defines a basic bottleneck structure.
# Arguments
inputs: Tensor, input tensor of conv layer.
filters: Integer, the dimensionality of the output space.
kernel: An integer or tuple/list of 2 integers, specifying the
width and height of the 2D convolution window.
t: Integer, expansion factor.
t is always applied to the input size.
s: An integer or tuple/list of 2 integers,specifying the strides
of the convolution along the width and height.Can be a single
integer to specify the same value for all spatial dimensions.
r: Boolean, Whether to use the residuals.
# Returns
Output tensor.
"""
tchannel = K.int_shape(inputs)[1] * expansion_factor
layer = _conv_block(inputs, tchannel, (1, 1), (1, 1))
layer = DepthwiseConv2D(kernel,
strides=(strides, strides),
depth_multiplier=1,
padding='same')(layer)
layer = BatchNormalization()(layer)
layer = relu6(layer)
layer = Conv2D(filters, (1, 1), strides=(1, 1), padding='same')(layer)
layer = BatchNormalization()(layer)
if residuals:
layer = add([layer, inputs])
return layer
def exponentialMap(args):
velo_raw = args
x, y, z = K.int_shape(args)[1:4]
# clip too large values:
v_max = 0.5 * (2**steps)
v_min = -v_max
velo = tf.clip_by_value(velo_raw, v_min, v_max)
# ij indexing doesn't change (x,y,z) to (y,x,z)
grid = tf.expand_dims(
tf.stack(
tf.meshgrid(tf.linspace(0., x - 1., x),
tf.linspace(0., y - 1., y),
tf.linspace(0., z - 1., z),
indexing='ij'), -1), 0)
# replicate along batch size
stacked_grids = tf.tile(grid, (tf.shape(velo)[0], 1, 1, 1, 1))
res = tfVectorFieldExp(velo, stacked_grids, n_steps=steps)
return res
def build(self,
block_config: tuple,
bottleneck: bool,
name: str = 'ResNet'):
"""
build a ResNet model
:param block_config: number blocks in stage 2 ~ 5
:param bottleneck: whether to use a bottleneck residual block
:param name: model name
:return: model
"""
self.bottleneck = bottleneck
img_input = Input(shape=self.input_shape)
# Stage 1
x = self.Conv2D(64, kernel_size=7, strides=2,
padding='same')(img_input)
x = self.BatchNormalization()(x)
x = Activation('relu')(x)
x = MaxPooling2D(pool_size=3, strides=2)(x)
# Stage 2 ~ 5
x = self.apply_residual_stage(x, 2, block_config[0])
x = self.apply_residual_stage(x, 3, block_config[1])
x = self.apply_residual_stage(x, 4, block_config[2])
x = self.apply_residual_stage(x, 5, block_config[3])
x = self.BatchNormalization()(x)
x = Activation('relu')(x)
shape = K.int_shape(x)
x = AveragePooling2D(pool_size=(shape[1], shape[2]), strides=1)(x)
x = Flatten()(x)
x = self.Dense(self.classes, 'softmax')(x)
return Model(inputs=img_input, outputs=x, name=name)
def get_constants(self, inputs, training=None):
constants = []
if self.implementation != 0 and 0 < self.dropout < 1:
input_shape = K.int_shape(inputs)
input_dim = input_shape[-1]
ones = K.ones_like(K.reshape(inputs[:, 0, 0], (-1, 1)))
ones = K.tile(ones, (1, int(input_dim)))
def dropped_inputs():
return K.dropout(ones, self.dropout)
dp_mask = [
K.in_train_phase(dropped_inputs, ones, training=training)
for _ in range(4)
]
constants.append(dp_mask)
else:
constants.append([K.cast_to_floatx(1.) for _ in range(4)])
if 0 < self.recurrent_dropout < 1:
ones = K.ones_like(K.reshape(inputs[:, 0, 0], (-1, 1)))
ones = K.tile(ones, (1, self.units))
def dropped_inputs():
return K.dropout(ones, self.recurrent_dropout)
rec_dp_mask = [
K.in_train_phase(dropped_inputs, ones, training=training)
for _ in range(4)
]
constants.append(rec_dp_mask)
else:
constants.append([K.cast_to_floatx(1.) for _ in range(4)])
# append the input as well for use later
constants.append(inputs)
return constants
def bottleneck_encoder(self,
tensor,
nfilters,
downsampling=False,
dilated=False,
asymmetric=False,
normal=False,
drate=0.1,
name=''):
"""
Encoder
:param tensor: input tensor
:param nfilters: Number of filters
:param downsampling: Downsample the feature map
:param dilated: determines if ther should be dilated convultion
:param asymmetric: Determines if there should be asymmetric convolution
:param normal: enables 3x3 convolution on feature map
:param drate: rate of dilation
:param name: the name for the weight variable.
:return: encoder output
"""
y = tensor
skip = tensor
stride = 1
ksize = 1
# Filters operating on downsampled images have a bigger receptive field and hence gathers more context.
if downsampling:
stride = 2
ksize = 2
skip = MaxPooling2D(pool_size=(2, 2),
name=f'max_pool_{name}')(skip)
skip = Permute(
(1, 3, 2),
name=f'permute_1_{name}')(skip) # (B, H, W, C) -> (B, H, C, W)
ch_pad = nfilters - K.int_shape(tensor)[-1]
skip = ZeroPadding2D(padding=((0, 0), (0, ch_pad)),
name=f'zeropadding_{name}')(skip)
skip = Permute(
(1, 3, 2),
name=f'permute_2_{name}')(skip) # (B, H, C, W) -> (B, H, W, C)
y = Conv2D(filters=nfilters // 4,
kernel_size=(ksize, ksize),
kernel_initializer='he_normal',
strides=(stride, stride),
padding='same',
use_bias=False,
name=f'1x1_conv_{name}')(y)
y = BatchNormalization(momentum=0.1, name=f'bn_1x1_{name}')(y)
y = PReLU(shared_axes=[1, 2], name=f'prelu_1x1_{name}')(y)
if normal:
# deconv with 3x3 filter
y = Conv2D(filters=nfilters // 4,
kernel_size=(3, 3),
kernel_initializer='he_normal',
padding='same',
name=f'3x3_conv_{name}')(y)
elif asymmetric:
# decompose 5x5 convolution to two asymmetric layers as 5x1 and 1x5
y = Conv2D(filters=nfilters // 4,
kernel_size=(5, 1),
kernel_initializer='he_normal',
padding='same',
use_bias=False,
name=f'5x1_conv_{name}')(y)
y = Conv2D(filters=nfilters // 4,
kernel_size=(1, 5),
kernel_initializer='he_normal',
padding='same',
name=f'1x5_conv_{name}')(y)
elif dilated:
y = Conv2D(filters=nfilters // 4,
kernel_size=(3, 3),
kernel_initializer='he_normal',
dilation_rate=(dilated, dilated),
padding='same',
name=f'dilated_conv_{name}')(y)
y = BatchNormalization(momentum=0.1, name=f'bn_main_{name}')(y)
y = PReLU(shared_axes=[1, 2], name=f'prelu_{name}')(y)
y = Conv2D(filters=nfilters,
kernel_size=(1, 1),
kernel_initializer='he_normal',
use_bias=False,
name=f'final_1x1_{name}')(y)
y = BatchNormalization(momentum=0.1, name=f'bn_final_{name}')(y)
y = SpatialDropout2D(rate=drate,
name=f'spatial_dropout_final_{name}')(y)
y = Add(name=f'add_{name}')([y, skip])
y = PReLU(shared_axes=[1, 2], name=f'prelu_out_{name}')(y)
return y
def step(self, inputs, states):
h_tm1 = states[0]
c_tm1 = states[1]
dp_mask = states[2]
rec_dp_mask = states[3]
x_input = states[4]
# alignment model
h_att = K.repeat(h_tm1, self.timestep_dim)
att = _time_distributed_dense(x_input,
self.attention_weights,
self.attention_bias,
output_dim=K.int_shape(
self.attention_weights)[1])
attention_ = self.attention_activation(
K.dot(h_att, self.attention_recurrent_weights) + att)
attention_ = K.squeeze(
K.dot(attention_, self.attention_recurrent_bias), 2)
alpha = K.exp(attention_)
if dp_mask is not None:
alpha *= dp_mask[0]
alpha /= K.sum(alpha, axis=1, keepdims=True)
alpha_r = K.repeat(alpha, self.input_dim)
alpha_r = K.permute_dimensions(alpha_r, (0, 2, 1))
# make context vector (soft attention after Bahdanau et al.)
z_hat = x_input * alpha_r
context_sequence = z_hat
z_hat = K.sum(z_hat, axis=1)
if self.implementation == 2:
z = K.dot(inputs * dp_mask[0], self.kernel)
z += K.dot(h_tm1 * rec_dp_mask[0], self.recurrent_kernel)
z += K.dot(z_hat, self.attention_kernel)
if self.use_bias:
z = K.bias_add(z, self.bias)
z0 = z[:, :self.units]
z1 = z[:, self.units:2 * self.units]
z2 = z[:, 2 * self.units:3 * self.units]
z3 = z[:, 3 * self.units:]
i = self.recurrent_activation(z0)
f = self.recurrent_activation(z1)
c = f * c_tm1 + i * self.activation(z2)
o = self.recurrent_activation(z3)
else:
if self.implementation == 0:
x_i = inputs[:, :self.units]
x_f = inputs[:, self.units:2 * self.units]
x_c = inputs[:, 2 * self.units:3 * self.units]
x_o = inputs[:, 3 * self.units:]
elif self.implementation == 1:
x_i = K.dot(inputs * dp_mask[0], self.kernel_i) + self.bias_i
x_f = K.dot(inputs * dp_mask[1], self.kernel_f) + self.bias_f
x_c = K.dot(inputs * dp_mask[2], self.kernel_c) + self.bias_c
x_o = K.dot(inputs * dp_mask[3], self.kernel_o) + self.bias_o
else:
raise ValueError('Unknown `implementation` mode.')
i = self.recurrent_activation(
x_i + K.dot(h_tm1 * rec_dp_mask[0], self.recurrent_kernel_i) +
K.dot(z_hat, self.attention_i))
f = self.recurrent_activation(
x_f + K.dot(h_tm1 * rec_dp_mask[1], self.recurrent_kernel_f) +
K.dot(z_hat, self.attention_f))
c = f * c_tm1 + i * self.activation(
x_c + K.dot(h_tm1 * rec_dp_mask[2], self.recurrent_kernel_c) +
K.dot(z_hat, self.attention_c))
o = self.recurrent_activation(
x_o + K.dot(h_tm1 * rec_dp_mask[3], self.recurrent_kernel_o) +
K.dot(z_hat, self.attention_o))
h = o * self.activation(c)
if 0 < self.dropout + self.recurrent_dropout:
h._uses_learning_phase = True
if self.return_attention:
return context_sequence, [h, c]
else:
return h, [h, c]
def generateAvgFromVolumes(vol_center, volumes, model):
session = tf.Session()
model_config = {
'batchsize': 1,
'split': 0.9,
'validation': 0.1,
'half_res': True,
'epochs': 200,
'groupnorm': True,
'GN_groups': 32,
'atlas': 'atlas.nii.gz',
'model_output': 'model.pkl',
'exponentialSteps': 7,
}
atlas, itk_atlas = DataGenerator.loadAtlas(model_config)
m = DiffeomorphicRegistrationNet.create_model(model_config)
m.load_weights(model)
shapes = atlas.squeeze().shape
print("First is : {}".format(vol_center))
vol_first = vol_center
np_vol_center = readNormalizedVolumeByPath(vol_first, itk_atlas).reshape(
1, *shapes).astype(np.float32)
velocities = []
for vol in volumes:
#np_atlas = atlas.reshape(1,*shapes).astype(np.float32)
np_vol = readNormalizedVolumeByPath(vol, itk_atlas).reshape(
1, *shapes).astype(np.float32)
np_stack = np.empty(1 * shapes[0] * shapes[1] * shapes[2] * 2,
dtype=np.float32).reshape(1, *shapes, 2)
np_stack[:, :, :, :, 0] = np_vol
np_stack[:, :, :, :, 1] = np_vol_center
#tf_stack = tf.convert_to_tensor(np_stack)
predictions = m.predict(np_stack)
velocity = predictions[2][0, :, :, :, :]
velocities.append(velocity)
# compute avg velocities
avg_velocity = np.zeros(
int(1 * shapes[0] / 2 * shapes[1] / 2 * shapes[2] / 2 * 3),
dtype=np.float32).reshape(1, *[int(s / 2) for s in shapes], 3)
for v in velocities:
avg_velocity += v
avg_velocity /= float(len(velocities))
# apply squaring&scaling
steps = model_config['exponentialSteps']
tf_velo = tf.convert_to_tensor(
avg_velocity.reshape(1, *[int(s / 2) for s in shapes], 3))
tf_vol_center = tf.convert_to_tensor(np_vol_center.reshape(1, *shapes, 1))
x, y, z = K.int_shape(tf_velo)[1:4]
# clip too large values:
v_max = 0.5 * (2**steps)
v_min = -v_max
velo = tf.clip_by_value(tf_velo, v_min, v_max)
# ij indexing doesn't change (x,y,z) to (y,x,z)
grid = tf.expand_dims(
tf.stack(
tf.meshgrid(tf.linspace(0., x - 1., x),
tf.linspace(0., y - 1., y),
tf.linspace(0., z - 1., z),
indexing='ij'), -1), 0)
# replicate along batch size
stacked_grids = tf.tile(grid, (tf.shape(velo)[0], 1, 1, 1, 1))
displacement = tfVectorFieldExpHalf(velo, stacked_grids, n_steps=steps)
displacement_highres = toUpscaleResampled(displacement)
# warp center volume
new_warped = remap3d(tf_vol_center, displacement_highres)
with session.as_default():
new_volume = new_warped.eval(session=session).reshape(*shapes)
vol_dirs = np.array(itk_atlas.GetDirection()).reshape(3, 3)
# reapply directions
warp_np = np.flip(new_volume,
[a for a in range(3) if vol_dirs[a, a] == -1.])
# prepare axes swap from xyz to zyx
warp_np = np.transpose(warp_np, (2, 1, 0))
# write image
warp_img = sitk.GetImageFromArray(warp_np)
warp_img.SetOrigin(itk_atlas.GetOrigin())
warp_img.SetDirection(itk_atlas.GetDirection())
sitk.WriteImage(warp_img, "new_volume.nii.gz")