FSL Brain Extraction Tool
[+ show/hide code]# Pilot imports
from caps.toy_datasets import get_sample_data
from capsul.study_config import StudyConfig
from capsul.utils.sorted_dictionary import SortedDictionary
from nsap.lib.base import ensure_is_dir
# Get toy dataset
toy_dataset = get_sample_data("mni_2mm")
# Create FSL brain extraction pipeline
bet_pipeline = BET()
# Print Input Spec
print bet_pipeline.get_input_spec()
# Initialize BET pipeline
bet_pipeline.input_file = toy_dataset.mni
# Execute the pipeline
bet_working_dir = os.path.join(working_dir, "bet")
ensure_is_dir(bet_working_dir)
default_config = SortedDictionary(
("output_directory", bet_working_dir),
("fsl_config", "/etc/fsl/4.1/fsl.sh"),
("use_fsl", True),
("use_smart_caching", True),
("generate_logging", True)
)
study = StudyConfig(default_config)
study.run(bet_pipeline)
# Print all pipeline outputs
print "\nOUTPUTS\n"
for trait_name, trait_value in bet_pipeline.get_outputs().iteritems():
print "{0}: {1}".format(trait_name, trait_value)