def init_spaces(checkpoint=True):
"""Initialize the :attr:`~workflow.spaces` setting."""
from niworkflows.utils.spaces import Reference, SpatialReferences
spaces = execution.output_spaces or SpatialReferences()
if not isinstance(spaces, SpatialReferences):
spaces = SpatialReferences([
ref for s in spaces.split(' ') for ref in Reference.from_string(s)
])
if checkpoint and not spaces.is_cached():
spaces.checkpoint()
# Add the default standard space if not already present (required by several sub-workflows)
if "MNI152NLin2009cAsym" not in spaces.get_spaces(nonstandard=False,
dim=(3, )):
spaces.add(Reference("MNI152NLin2009cAsym", {}))
# Ensure user-defined spatial references for outputs are correctly parsed.
# Certain options require normalization to a space not explicitly defined by users.
# These spaces will not be included in the final outputs.
if workflow.use_aroma:
# Make sure there's a normalization to FSL for AROMA to use.
spaces.add(Reference("MNI152NLin6Asym", {"res": "2"}))
cifti_output = workflow.cifti_output
if cifti_output:
# CIFTI grayordinates to corresponding FSL-MNI resolutions.
vol_res = '2' if cifti_output == '91k' else '1'
spaces.add(Reference("fsaverage", {"den": "164k"}))
spaces.add(Reference("MNI152NLin6Asym", {"res": vol_res}))
# Make the SpatialReferences object available
workflow.spaces = spaces
def init_spaces(checkpoint=True):
"""Initialize the :attr:`~workflow.spaces` setting."""
from niworkflows.utils.spaces import Reference, SpatialReferences
spaces = execution.output_spaces or SpatialReferences()
if not isinstance(spaces, SpatialReferences):
spaces = SpatialReferences(
[ref for s in spaces.split(' ')
for ref in Reference.from_string(s)]
)
if checkpoint and not spaces.is_cached():
spaces.checkpoint()
# Add the default standard space if not already present (required by several sub-workflows)
if "Fischer344" not in spaces.get_spaces(nonstandard=False, dim=(3,)):
spaces.add(
Reference("Fischer344", {})
)
# Make the SpatialReferences object available
workflow.spaces = spaces