# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-# vi: set ft=python sts=4 ts=4 sw=4 et:## Copyright 2021 The NiPreps Developers <nipreps@gmail.com>## Licensed under the Apache License, Version 2.0 (the "License");# you may not use this file except in compliance with the License.# You may obtain a copy of the License at## http://www.apache.org/licenses/LICENSE-2.0## Unless required by applicable law or agreed to in writing, software# distributed under the License is distributed on an "AS IS" BASIS,# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.# See the License for the specific language governing permissions and# limitations under the License.## We support and encourage derived works from this project, please read# about our expectations at## https://www.nipreps.org/community/licensing/#"""Run the BOLD reference+mask workflow"""importos
[docs]defget_parser():"""Build parser object."""fromargparseimportArgumentParserfromargparseimportRawTextHelpFormatter,RawDescriptionHelpFormatterparser=ArgumentParser(description="""NiWorkflows Utilities""",formatter_class=RawTextHelpFormatter)subparsers=parser.add_subparsers(dest="command")be_parser=subparsers.add_parser("brain-extract",formatter_class=RawDescriptionHelpFormatter,description="""Execute brain extraction and related operations (e.g., \intensity nonuniformity correction, robust averaging, etc.)""",)be_parser.add_argument("input_file",action="store",help="the input file")be_parser.add_argument("out_path",action="store",help="the output directory")be_parser.add_argument("--modality","-m",action="store",choices=("bold","t1w"),default="bold",help="the input file",)parser.add_argument("--omp-nthreads",action="store",type=int,default=os.cpu_count(),help="Number of CPUs available to individual processes",)parser.add_argument("--nprocs",action="store",type=int,default=os.cpu_count(),help="Number of processes that may run in parallel",)returnparser