Source code for fsl.wrappers.fugue

#
# fugue.py - Wrappers for fugue/field map tools.
#
# Author: Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk>
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
"""This module contains wrappers for the FSL `FUGUE
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE>`_ tools, for EPI field map
processing and distortion correction.
"""


from . import wrapperutils as wutils


[docs]@wutils.fileOrImage('in', 'unwarp', 'warp', 'phasemap', 'savefmap', 'loadfmap', 'saveshift', 'loadshift', 'mask') @wutils.fslwrapper def fugue(input=None, **kwargs): """Wrapper for the ``fugue`` command.""" argmap = { 'input' : 'in' } valmap = { 'dwelltoasym' : wutils.SHOW_IF_TRUE, 'median' : wutils.SHOW_IF_TRUE, 'despike' : wutils.SHOW_IF_TRUE, 'nofill' : wutils.SHOW_IF_TRUE, 'noextend' : wutils.SHOW_IF_TRUE, 'pava' : wutils.SHOW_IF_TRUE, 'phaseconj' : wutils.SHOW_IF_TRUE, 'icorr' : wutils.SHOW_IF_TRUE, 'icorronly' : wutils.SHOW_IF_TRUE, 'unmaskfmap' : wutils.SHOW_IF_TRUE, 'unmaskshift' : wutils.SHOW_IF_TRUE, 'nokspace' : wutils.SHOW_IF_TRUE, 'nocheck' : wutils.SHOW_IF_TRUE, 'verbose' : wutils.SHOW_IF_TRUE, } kwargs.update({'input' : input}) cmd = ['fugue'] + wutils.applyArgStyle('--=', argmap=argmap, valmap=valmap, **kwargs) return cmd
[docs]@wutils.fileOrImage('input', 'mask', 'sigloss') @wutils.fslwrapper def sigloss(input, sigloss, **kwargs): """Wrapper for the ``sigloss`` command.""" valmap = {'verbose' : wutils.SHOW_IF_TRUE} cmd = ['sigloss', '--in', input, '--sigloss', sigloss] cmd += wutils.applyArgStyle('--', valmap=valmap, **kwargs) return cmd
[docs]@wutils.fileOrImage('complex', 'abs', 'phase', 'mask', 'out', 'unwrap', 'savemask', 'rawphase', 'labels') @wutils.fslwrapper def prelude(**kwargs): """Wrapper for the ``sigloss`` command.""" valmap = { 'labelslices' : wutils.SHOW_IF_TRUE, 'slices' : wutils.SHOW_IF_TRUE, 'force3D' : wutils.SHOW_IF_TRUE, 'removeramps' : wutils.SHOW_IF_TRUE, 'verbose' : wutils.SHOW_IF_TRUE, } cmd = ['prelude'] + wutils.applyArgStyle('--=', valmap=valmap, **kwargs) return cmd
[docs]@wutils.fileOrImage('phase_image', 'magnitude_image', 'out_image') @wutils.fslwrapper def fsl_prepare_fieldmap(phase_image, magnitude_image, out_image, deltaTE, scanner=None, **kwargs): """Wrapper for the ``fsl_prepare_fieldmap`` command. <scanner> defaults to 'SIEMENS'""" if scanner is None: scanner = 'SIEMENS' valmap = { 'nocheck' : wutils.SHOW_IF_TRUE, } cmd = ['fsl_prepare_fieldmap', scanner, phase_image, magnitude_image, out_image, str(deltaTE)] cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs) return cmd