Coregistration 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_src_dataset = get_sample_data("mni_1mm")
toy_dest_dataset = get_sample_data("mni_2mm")
# Create
coreg_pipeline = Coregistration()
# Print Input Spec
print coreg_pipeline.get_input_spec()
# Initialize Coregistration pipeline
coreg_pipeline.moving_image = toy_src_dataset.mni
coreg_pipeline.reference_image = toy_dest_dataset.mni
# Execute the pipeline
coreg_working_dir = os.path.join(working_dir, "coregistration")
ensure_is_dir(coreg_working_dir)
default_config = SortedDictionary(
("output_directory", coreg_working_dir),
("spm_directory", "/i2bm/local/spm8"),
("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(coreg_pipeline)
# Print all pipeline outputs
print "\nOUTPUTS\n"
for trait_name, trait_value in coreg_pipeline.get_outputs().iteritems():
print "{0}: {1}".format(trait_name, trait_value)