SPM Smoothing Tool
[+ show/hide code]# Pilot imports
from capsul.study_config import StudyConfig
from capsul.utils.sorted_dictionary import SortedDictionary
from nsap.lib.base import ensure_is_dir
from caps.toy_datasets import get_sample_data
# Get toy dataset
toy_dataset = get_sample_data("localizer")
# Create FSL brain extraction pipeline
norm_pipeline = Normalization()
# Print Input Spec
print norm_pipeline.get_input_spec()
# Initialize Normalization pipeline
norm_pipeline.coregistered_struct_image = toy_dataset.mean
norm_pipeline.func_image = toy_dataset.fmri
print "SWITCH EVENT"
norm_pipeline.select_normalization = "segment"
print (norm_pipeline.nodes["select_normalization"].switch)
# Execute the pipeline
norm_working_dir = os.path.join(working_dir, "normalization")
ensure_is_dir(norm_working_dir)
default_config = SortedDictionary(
("output_directory", norm_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(norm_pipeline)
# Print all pipeline outputs
print "\nOUTPUTS\n"
for trait_name, trait_value in norm_pipeline.get_outputs().iteritems():
print "{0}: {1}".format(trait_name, trait_value)