Source code for fsl.wrappers.fsl_anat

#
# fsl_anat.py - Wrapper for the FSL_ANAT command.
#
# Author: Martin Craig <martin.craig@eng.ox.ac.uk>
#
"""This module provides the :func:`fsl_anat` function, a wrapper for the FSL
`FSL_ANAT <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/fsl_anat>`_ command.
"""

import fsl.utils.assertions as asrt
from . import wrapperutils  as wutils

[docs]@wutils.fileOrImage('img', outprefix='out') @wutils.fslwrapper def fsl_anat(img, out='fsl_anat', **kwargs): """Wrapper for the ``fsl_anat`` command. :arg img: Input structural image :arg out: Output directory name """ asrt.assertIsNifti(img) valmap = { 'strongbias' : wutils.SHOW_IF_TRUE, 'weakbias' : wutils.SHOW_IF_TRUE, 'noreorient' : wutils.SHOW_IF_TRUE, 'nocrop' : wutils.SHOW_IF_TRUE, 'nobias' : wutils.SHOW_IF_TRUE, 'noreg' : wutils.SHOW_IF_TRUE, 'nononlinreg' : wutils.SHOW_IF_TRUE, 'noseg' : wutils.SHOW_IF_TRUE, 'nosubcortseg' : wutils.SHOW_IF_TRUE, 'nosearch' : wutils.SHOW_IF_TRUE, 'nocleanup' : wutils.SHOW_IF_TRUE, } argmap = { } img_type = kwargs.pop("img_type", "T1") cmd = ['fsl_anat', '-i', img, '-o', out, '-t', img_type] smoothing = kwargs.pop("bias_smoothing", None) if smoothing is not None: cmd += ['-s', str(smoothing)] cmd += wutils.applyArgStyle('--=', valmap=valmap, argmap=argmap, singlechar_args=True, **kwargs) return cmd