Source code for fsl.wrappers.bet

#
# bet.py - Wrapper for the FSL bet command.
#
# Author: Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
# Author: Martin Craig <martin.craig@eng.ox.ac.uk>
#
"""This module provides the :func:`bet` function, a wrapper for the FSL
`BET <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET>`_ command.
"""


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


[docs]@wutils.fileOrImage('input', outprefix='output') @wutils.fslwrapper def bet(input, output, **kwargs): """Wrapper for the ``bet`` command. :arg mask: Generate a brain mask :arg seg: If ``False``, a brain extracted image is not generated. :arg robust: Robust brain centre estimation :arg fracintensity: Fractional intensity threshold Refer to the ``bet`` command-line help for details on all arguments. """ asrt.assertIsNifti(input) argmap = { 'mask' : 'm', 'robust' : 'R', 'fracintensity' : 'f', 'seg' : 'n', 'centre' : 'c', } valmap = { 'm' : wutils.SHOW_IF_TRUE, 'o' : wutils.SHOW_IF_TRUE, 's' : wutils.SHOW_IF_TRUE, 'n' : wutils.HIDE_IF_TRUE, 't' : wutils.SHOW_IF_TRUE, 'e' : wutils.SHOW_IF_TRUE, 'R' : wutils.SHOW_IF_TRUE, 'S' : wutils.SHOW_IF_TRUE, 'B' : wutils.SHOW_IF_TRUE, 'Z' : wutils.SHOW_IF_TRUE, 'F' : wutils.SHOW_IF_TRUE, 'A' : wutils.SHOW_IF_TRUE, 'v' : wutils.SHOW_IF_TRUE, 'd' : wutils.SHOW_IF_TRUE, } cmd = ['bet', input, output] # The 'centre' argument requires three co-ordinates and can't be passed # as a single value, so needs to be handled separately. Assume it is # passed as a Python sequence centre = kwargs.pop("c", None) if centre is not None: cmd += ['-c', ] + [str(v) for v in centre] cmd += wutils.applyArgStyle('-', argmap=argmap, valmap=valmap, **kwargs) return cmd
[docs]@wutils.fileOrImage('input', 'output') @wutils.fileOrArray('matrix') @wutils.fslwrapper def robustfov(input, output=None, **kwargs): """Wrapper for the ``robustfov`` command. """ asrt.assertIsNifti(input) if output is not None: kwargs.update({'output' : output}) argmap = { 'output' : 'r', 'matrix' : 'm' } cmd = ['robustfov', '-i', input] cmd += wutils.applyArgStyle('-', argmap=argmap, **kwargs) return cmd