Warning: This document is for an old version of niworkflows.

Source code for niworkflows.cli.boldref

# 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,
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"""Run the BOLD reference+mask workflow"""
import os

[docs]def get_parser(): """Build parser object.""" from argparse import ArgumentParser from argparse import RawTextHelpFormatter, RawDescriptionHelpFormatter parser = 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", ) return parser
[docs]def main(args=None): """Entry point.""" from nipype.utils.filemanip import hash_infile from ..func.util import init_bold_reference_wf opts = get_parser().parse_args(args=args) wf = init_bold_reference_wf( opts.omp_nthreads, gen_report=True, name=hash_infile(opts.input_file), ) wf.inputs.inputnode.bold_file = opts.input_file wf.base_dir = os.getcwd() plugin = { "plugin": "MultiProc", "plugin_args": {"nprocs": opts.nprocs}, } if opts.nprocs < 2: plugin = {"plugin": "Linear"} wf.run(**plugin)
if __name__ == "__main__": from sys import argv main(args=argv[1:])