else:
run_workflow(template, plugin=subj_pipeline_options['plugin_name'], plugin_args=subj_pipeline_options['plugin_args'])
if __name__ == '__main__':
import sys
from AutoWorkup import setup_environment
from docopt import docopt
argv = docopt(__doc__, version='1.1')
print(argv)
if argv['--workphase'] != 'subject-template-generation':
print("ERROR: Only --workphase subject-template-generation supported for template building")
sys.exit(-1)
print('=' * 100)
environment, experiment, pipeline, cluster = setup_environment(argv)
from nipype import config as nipype_config
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
from nipype.interfaces.utility import IdentityInterface, Function
import nipype.interfaces.ants as ants
from PipeLineFunctionHelpers import ConvertSessionsListOfPosteriorListToDictionaryOfSessionLists
from workflows.atlasNode import MakeAtlasNode, CreateAtlasXMLAndCleanedDeformedAverages
from utilities.misc import GenerateSubjectOutputPattern as outputPattern
from utilities.distributed import modify_qsub_args
from workflows.utils import run_workflow, print_workflow
from BAWantsRegistrationBuildTemplate import BAWantsRegistrationTemplateBuildSingleIterationWF
from utilities.configFileParser import nipype_options
from nipype.interfaces.semtools.testing.generateaveragelmkfile import GenerateAverageLmkFile
exit = _template_runner(argv, environment, experiment, pipeline, cluster)
hasHeader=kwargs["--header"],
)
def _test():
"""
Tests doc
"""
import doctest
doctest.testmod(verbose=True)
return 0
if __name__ == "__main__":
import sys
from docopt import docopt
argv = docopt(__doc__, version="1.1")
print(argv)
print(("=" * 100))
from AutoWorkup import setup_environment
if argv["--test"]:
sys.exit(_test())
environment, experiment, pipeline, cluster = setup_environment(argv)
# from AutoWorkup import setup_environment
# environment, experiment, pipeline, cluster = setup_envir""
sys.exit(main(environment, experiment, pipeline, cluster, **argv))