SPM Smoothing 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
smooth_pipeline = Smoothing()
# Print Input Spec
print smooth_pipeline.get_input_spec()
# Initialize Smoothing pipeline
smooth_pipeline.input_image = toy_dataset.mni
# Execute the pipeline
smooth_working_dir = os.path.join(working_dir, "smoothing")
ensure_is_dir(smooth_working_dir)
default_config = SortedDictionary(
("output_directory", smooth_working_dir),
("spm_directory", "/i2bm/local/spm8-5236"),
("matlab_exec", "/neurospin/local/bin/matlab"),
("spm_exec_cmd", "/i2bm/local/bin/spm8"),
("use_spm_mcr", False),
("use_smart_caching", True),
("generate_logging", True)
)
study = StudyConfig(default_config)
study.run(smooth_pipeline)
# Print all pipeline outputs
print "\nOUTPUTS\n"
for trait_name, trait_value in smooth_pipeline.get_outputs().iteritems():
print "{0}: {1}".format(trait_name, trait_value)