def __init__(self,
ants_image=[[0.0]],
mask_ants=[[0.0]],
**options):
import ants
self.atropos = ants.atropos(a = ants_image,
x = mask_ants,
**options)
def __segmentation(self):
logger.info("computing GM, WM, CSF segmentation")
print("computing GM, WM, CSF segmentation")
# https://antsx.github.io/ANTsPyNet/docs/build/html/utilities.html#applications
priors = {
"csf":
os.path.join('./templates',
'mni_icbm152_csf_tal_nlin_sym_09a.nii.gz'),
"gm":
os.path.join('./templates',
'mni_icbm152_gm_tal_nlin_sym_09a.nii.gz'),
"wm":
os.path.join('./templates',
'mni_icbm152_wm_tal_nlin_sym_09a.nii.gz')
}
# list_of_priors = (ants.image_read(priors['csf']), ants.image_read(priors['gm']), ants.image_read(priors['wm']))
if self._t1file != None and self._t2file != None:
# segm = deep_atropos(self._t1_n4 * self._mask, do_preprocessing=False, use_spatial_priors=0, verbose=False)
# self._segm = segm['segmentation_image']
segm = ants.atropos(a=(self._t1_n4, self._t2_n4),
i='Kmeans[3]',
m='[0.2,1x1x1]',
c='[3,0]',
x=self._mask)
self._segm = segm['segmentation']
self._gm = np.where((self._segm.numpy() == 2), 1,
0).astype('float32')
self._wm = np.where((self._segm.numpy() == 3), 1,
0).astype('float32')
if self._t1file != None and self._t2file == None:
# segm = deep_atropos(self._t1_n4 * self._mask, do_preprocessing=False, use_spatial_priors=0, verbose=False)
# self._segm = segm['segmentation_image']
segm = ants.atropos(a=self._t1_n4,
i='Kmeans[3]',
m='[0.2,1x1x1]',
c='[3,0]',
x=self._mask)
self._segm = segm['segmentation']
self._gm = np.where((self._segm.numpy() == 2), 1,
0).astype('float32')
self._wm = np.where((self._segm.numpy() == 3), 1,
0).astype('float32')
def test_multiple_inputs(self):
img = ants.image_read(ants.get_ants_data("r16"))
img = ants.resample_image(img, (64, 64), 1, 0)
mask = ants.get_mask(img)
segs1 = ants.atropos(a=img,
m='[0.2,1x1]',
c='[2,0]',
i='kmeans[3]',
x=mask)
# Use probabilities from k-means seg as priors
segs2 = ants.atropos(a=img,
m='[0.2,1x1]',
c='[2,0]',
i=segs1['probabilityimages'],
x=mask)
# multiple inputs
feats = [img, ants.iMath(img, "Laplacian"), ants.iMath(img, "Grad")]
segs3 = ants.atropos(a=feats,
m='[0.2,1x1]',
c='[2,0]',
i=segs1['probabilityimages'],
x=mask)
link = '/ROBEX_Output/'
# Skull stripped data output by ROBEX
mylist = os.listdir('/ROBEX_Output/')
# fixed image is the template to which the registration will be fitted found in the downloaded ANTs package
fixed = ants.image_read('/ANTsPy-master/data/mni.nii.gz')
# This runs the entire dataset through registration
for i in mylist:
#registraction
moving = ants.image_read('/arc/project/ex-rtam-1/BrainExt_AllData/' + i)
mytx = ants.registration(fixed=fixed,
moving=moving,
type_of_transform='SyNAggro')
mywarpedimage = ants.apply_transforms(fixed=fixed,
moving=moving,
transformlist=mytx['fwdtransforms'])
mywarpedimage.to_file('/Output_ants_SyNAggro/Registration/' + i)
#segmentation
mask = ants.get_mask(mywarpedimage)
img_seg = ants.atropos(a=mywarpedimage,
m='[0.2,1x1x1]',
c='[2,0]',
i='kmeans[3]',
x=mask)
gm = img_seg['probabilityimages'][1]
gm.to_file('/Output_ants_SyNAggro/Greymatter/' + i)
continue
os.mkdir( outputDirectory )
outputPrefix = outputDirectory + 'antspy'
numberOfOuterIterations = 5
image = ants.image_read( dataDirectory + 'KKI2009-01-MPRAGE_slice150.nii.gz', dimension = 2 )
mask = ants.image_read( dataDirectory + 'KKI2009-01-MPRAGE_slice150_mask.nii.gz', dimension = 2 )
weightMask = None
for i in range( numberOfOuterIterations ):
print( "*************** N4 <---> Atropos iteration ", i, " ******************\n" )
n4Results = ants.n4_bias_field_correction( image, mask = mask,
weight_mask = weightMask, verbose = True )
image = n4Results
atroposResults = ants.atropos( a = image, x = mask )
onesImage = ants.make_image( image.shape, voxval = 0,
spacing = ants.get_spacing( image ),
origin = ants.get_origin( image ),
direction = ants.get_direction( image ) )
weightMask = atroposResults['probabilityimages'][1] *\
( onesImage - atroposResults['probabilityimages'][0] ) *\
( onesImage - atroposResults['probabilityimages'][2] ) +\
atroposResults['probabilityimages'][2] *\
( onesImage - atroposResults['probabilityimages'][1] ) *\
( onesImage - atroposResults['probabilityimages'][0] )
ants.image_write( image, outputPrefix + "N4Corrected.nii.gz" )
ants.image_write( atroposResults['segmentation'], outputPrefix + "AtroposSegmentation.nii.gz" )
for i in range( len( atroposResults['probabilityimages'] ) ):
def test_example(self):
# test ANTsPy/ANTsR example
img = ants.image_read(ants.get_ants_data('r16'))
img = ants.resample_image(img, (64, 64), 1, 0)
mask = ants.get_mask(img)
ants.atropos(a=img, m='[0.2,1x1]', c='[2,0]', i='kmeans[3]', x=mask)
def longitudinal_cortical_thickness(t1s,
initial_template="oasis",
number_of_iterations=1,
refinement_transform="antsRegistrationSyNQuick[a]",
antsxnet_cache_directory=None,
verbose=False):
"""
Perform KellyKapowski cortical thickness longitudinally using \code{deepAtropos}
for segmentation of the derived single-subject template. It takes inspiration from
the work described here:
https://pubmed.ncbi.nlm.nih.gov/31356207/
Arguments
---------
t1s : list of ANTsImage
Input list of 3-D unprocessed t1-weighted brain images from a single subject.
initial_template : string or ANTsImage
Input image to define the orientation of the SST. Can be a string (see
get_antsxnet_data) or a specified template. This allows the user to create a
SST outside of this routine.
number_of_iterations : int
Defines the number of iterations for refining the SST.
refinement_transform : string
Transform for defining the refinement registration transform. See options in
ants.registration.
antsxnet_cache_directory : string
Destination directory for storing the downloaded template and model weights.
Since these can be resused, if is None, these data will be downloaded to a
~/.keras/ANTsXNet/.
verbose : boolean
Print progress to the screen.
Returns
-------
Cortical thickness image and segmentation probability images.
Example
-------
>>> t1s = list()
>>> t1s.append(ants.image_read("t1w_image.nii.gz"))
>>> kk = longitudinal_cortical_thickness(image)
"""
from ..utilities import get_antsxnet_data
from ..utilities import preprocess_brain_image
from ..utilities import deep_atropos
###################
#
# Initial SST + optional affine refinement
#
##################
sst = None
if isinstance(initial_template, str):
template_file_name_path = get_antsxnet_data(initial_template, antsxnet_cache_directory=antsxnet_cache_directory)
sst = ants.image_read(template_file_name_path)
else:
sst = initial_template
for s in range(number_of_iterations):
if verbose:
print("Refinement iteration", s, "( out of", number_of_iterations, ")")
sst_tmp = ants.image_clone(sst) * 0
for i in range(len(t1s)):
if verbose:
print("***************************")
print( "SST processing image", i, "( out of", len(t1s), ")")
print( "***************************" )
transform_type = "antsRegistrationSyNQuick[r]"
if s > 0:
transform_type = refinement_transform
t1_preprocessed = preprocess_brain_image(t1s[i],
truncate_intensity=(0.01, 0.99),
do_brain_extraction=False,
template=sst,
template_transform_type=transform_type,
do_bias_correction=False,
do_denoising=False,
intensity_normalization_type="01",
antsxnet_cache_directory=antsxnet_cache_directory,
verbose=verbose)
sst_tmp += t1_preprocessed['preprocessed_image']
sst = sst_tmp / len(t1s)
###################
#
# Preprocessing and affine transform to final SST
#
##################
t1s_preprocessed = list()
for i in range(len(t1s)):
if verbose:
print("***************************")
print( "Final processing image", i, "( out of", len(t1s), ")")
print( "***************************" )
t1_preprocessed = preprocess_brain_image(t1s[i],
truncate_intensity=(0.01, 0.99),
do_brain_extraction=True,
template=sst,
template_transform_type="antsRegistrationSyNQuick[a]",
do_bias_correction=True,
do_denoising=True,
intensity_normalization_type="01",
antsxnet_cache_directory=antsxnet_cache_directory,
verbose=verbose)
t1s_preprocessed.append(t1_preprocessed)
###################
#
# Deep Atropos of SST for priors
#
##################
sst_atropos = deep_atropos(sst, do_preprocessing=True,
antsxnet_cache_directory=antsxnet_cache_directory, verbose=verbose)
###################
#
# Traditional Atropos + KK for each iamge
#
##################
return_list = list()
for i in range(len(t1s_preprocessed)):
if verbose:
print("Atropos for image", i, "( out of", len(t1s), ")")
atropos_output = ants.atropos(t1s_preprocessed[i]['preprocessed_image'],
x=t1s_preprocessed[i]['brain_mask'], i=sst_atropos['probability_images'][1:7],
m="[0.1,1x1x1]", c="[5,0]", priorweight=0.5, p="Socrates[1]", verbose=int(verbose))
kk_segmentation = ants.image_clone(atropos_output['segmentation'])
kk_segmentation[kk_segmentation == 4] = 3
gray_matter = atropos_output['probabilityimages'][1]
white_matter = atropos_output['probabilityimages'][2] + atropos_output['probabilityimages'][3]
kk = ants.kelly_kapowski(s=kk_segmentation, g=gray_matter, w=white_matter,
its=45, r=0.025, m=1.5, x=0, verbose=int(verbose))
t1_dict = {'preprocessed_image' : t1s_preprocessed[i]['preprocessed_image'],
'thickness_image' : kk,
'segmentation_image' : atropos_output['segmentation'],
'csf_probability_image' : atropos_output['probabilityimages'][0],
'gray_matter_probability_image' : atropos_output['probabilityimages'][1],
'white_matter_probability_image' : atropos_output['probabilityimages'][2],
'deep_gray_matter_probability_image' : atropos_output['probabilityimages'][3],
'brain_stem_probability_image' : atropos_output['probabilityimages'][4],
'cerebellum_probability_image' : atropos_output['probabilityimages'][5],
'template_transforms' : t1s_preprocessed[i]['template_transforms']
}
return_list.append(t1_dict)
return_list.append(sst)
return(return_list)