def require_deep_gray_matter_mask(config,
section,
config_vars,
stack,
verbose=0):
"""Create deep gray matter mask from segmentation if none provided."""
deep_gray_matter_mask = config.get(section,
'deep_gray_matter_mask',
vars=config_vars)
if os.path.isfile(deep_gray_matter_mask):
return deep_gray_matter_mask
if verbose > 0:
print("Creating deep gray matter mask from segmentation image")
segmentation = config.get(section, 'input_tissues_image', vars=config_vars)
if not os.path.isfile(segmentation):
segmentation = config.get(section,
'input_labels_image',
vars=config_vars)
if not segmentation or not os.path.isfile(segmentation):
raise Exception("Input brain segmentation required")
neoctx.binarize(name=deep_gray_matter_mask,
segmentation=segmentation,
labels=get_labels(config, section,
'deep_gray_matter_labels'),
image=config.get(section, 'brain_mask', vars=config_vars),
temp=config.get(section, 'temp_dir', vars=config_vars))
if stack:
return neoctx.push_output(stack, deep_gray_matter_mask)
else:
return deep_gray_matter_mask
def require_brain_mask(config,
section,
config_vars,
stack,
verbose=0,
keep_regions_mask=False):
"""Resample input brain mask to standard RAS space."""
brain_mask = config.get(section, 'brain_mask', vars=config_vars)
if os.path.isfile(brain_mask):
return brain_mask
require_input_brain_mask(config, section, config_vars, stack, verbose)
if keep_regions_mask:
require_regions_mask(config, section, config_vars, None, verbose)
else:
require_regions_mask(config, section, config_vars, stack, verbose)
if verbose > 0:
print("Resampling brain mask to standard RAS space")
neoctx.binarize(name=brain_mask,
segmentation=config.get(section,
'input_brain_mask',
vars=config_vars),
image=config.get(section, 'regions_mask',
vars=config_vars),
threshold=0,
temp=config.get(section, 'temp_dir', vars=config_vars))
if stack:
brain_mask = neoctx.push_output(stack, brain_mask)
neoctx.run('close-image',
args=[brain_mask, brain_mask],
opts={'iterations': 5})
return brain_mask
def optional_corpus_callosum_mask(config,
section,
config_vars,
stack,
verbose=0):
"""Create corpus callosum mask from segmentation if none provided."""
corpus_callosum_mask = config.get(section,
'corpus_callosum_mask',
vars=config_vars)
if os.path.isfile(corpus_callosum_mask):
return corpus_callosum_mask
if verbose > 0:
print("Creating corpus callosum mask from segmentation image")
segmentation = config.get(section, 'input_labels_image', vars=config_vars)
if segmentation and os.path.isfile(segmentation):
require_brain_mask(config, section, config_vars, stack, verbose)
neoctx.binarize(name=corpus_callosum_mask,
segmentation=segmentation,
labels=get_labels(config, section,
'corpus_callosum_labels'),
image=config.get(section,
'brain_mask',
vars=config_vars),
temp=config.get(section, 'temp_dir', vars=config_vars))
if stack:
return neoctx.push_output(stack, corpus_callosum_mask)
else:
return corpus_callosum_mask
else:
return None
def require_input_brain_mask(config, section, config_vars, stack, verbose=0):
"""Create brain mask from segmentation if none provided."""
input_brain_mask = config.get(section, 'input_brain_mask', vars=config_vars)
if os.path.isfile(input_brain_mask):
return input_brain_mask
if verbose > 0:
print("Creating brain mask from segmentation image")
segmentation = config.get(section, 'input_labels_image', vars=config_vars)
if not segmentation or not os.path.isfile(segmentation):
segmentation = config.get(section, 'input_tissues_image', vars=config_vars)
if not segmentation or not os.path.isfile(segmentation):
raise Exception("Input brain segmentation required")
neoctx.binarize(
name=input_brain_mask,
segmentation=segmentation,
temp=config.get(section, 'temp_dir', vars=config_vars)
)
return neoctx.push_output(stack, input_brain_mask)
