diff --git a/fsl/wrappers/__init__.py b/fsl/wrappers/__init__.py index a27daebbf07c2e05a96f517b683b6e2af1630206..1ab959245d8caa3c5e094a39e85193902b69e123 100755 --- a/fsl/wrappers/__init__.py +++ b/fsl/wrappers/__init__.py @@ -97,39 +97,40 @@ decorators. """ -from fsl.wrappers.wrapperutils import (LOAD,) -from fsl.wrappers.bet import (bet, +from fsl.wrappers.wrapperutils import (LOAD,) +from fsl.wrappers.bet import (bet, robustfov) -from fsl.wrappers.eddy import (eddy, +from fsl.wrappers.eddy import (eddy, eddy_cuda, topup, applytopup) -from fsl.wrappers.fast import (fast,) -from fsl.wrappers.fsl_anat import (fsl_anat,) -from fsl.wrappers.fsl_sub import (fsl_sub,) -from fsl.wrappers.flirt import (flirt, +from fsl.wrappers.fast import (fast,) +from fsl.wrappers.fsl_anat import (fsl_anat,) +from fsl.wrappers.fsl_sub import (fsl_sub,) +from fsl.wrappers.flirt import (flirt, invxfm, applyxfm, applyxfm4D, concatxfm, mcflirt) -from fsl.wrappers.fnirt import (fnirt, +from fsl.wrappers.fnirt import (fnirt, applywarp, invwarp, convertwarp) -from fsl.wrappers.fslmaths import (fslmaths,) -from fsl.wrappers.fslstats import (fslstats,) -from fsl.wrappers.fugue import (fugue, +from fsl.wrappers.fslmaths import (fslmaths,) +from fsl.wrappers.fslstats import (fslstats,) +from fsl.wrappers.fugue import (fugue, prelude, sigloss, fsl_prepare_fieldmap) -from fsl.wrappers.melodic import (melodic, +from fsl.wrappers.melodic import (melodic, fsl_regfilt) -from fsl.wrappers.misc import (fslreorient2std, +from fsl.wrappers.misc import (fslreorient2std, fslorient, fslroi, slicer, cluster, gps) -from fsl.wrappers.epi_reg import epi_reg -from fsl.wrappers import tbss +from fsl.wrappers.epi_reg import epi_reg +from fsl.wrappers import tbss +from fsl.wrappers.standard_space_roi import standard_space_roi diff --git a/fsl/wrappers/standard_space_roi.py b/fsl/wrappers/standard_space_roi.py index bc0e584c18a4a6739ffeac10ce9b9dc2d73c5908..4b402ec696b00eff8b993144f699182b88e2bb43 100644 --- a/fsl/wrappers/standard_space_roi.py +++ b/fsl/wrappers/standard_space_roi.py @@ -11,7 +11,7 @@ the FSL `standard_space_roi`_ command. import fsl.utils.assertions as asrt from . import wrapperutils as wutils -@wutils.fileOrImage('input', 'maskMASK', 'roiMASK', 'ssref', 'altinput',outprefix='output') +@wutils.fileOrImage('input', 'output', 'maskMASK', 'roiMASK', 'ssref', 'altinput') @wutils.fslwrapper def standard_space_roi(input, output, **kwargs): """Wrapper for the ``standard_space_roi`` command. @@ -33,17 +33,30 @@ def standard_space_roi(input, output, **kwargs): """ asrt.assertIsNifti(input) + argmap = { + 'twod' : '2D' + } + valmap = { - 'maskFOV' : wutils.SHOW_IF_TRUE, - 'maskNONE' : wutils.SHOW_IF_TRUE, - 'roiFOV' : wutils.SHOW_IF_TRUE, - 'roiNONE' : wutils.SHOW_IF_TRUE, - 'd' : wutils.SHOW_IF_TRUE, - 'b' : wutils.SHOW_IF_TRUE, + 'maskFOV' : wutils.SHOW_IF_TRUE, + 'maskNONE' : wutils.SHOW_IF_TRUE, + 'roiFOV' : wutils.SHOW_IF_TRUE, + 'roiNONE' : wutils.SHOW_IF_TRUE, + 'd' : wutils.SHOW_IF_TRUE, + 'b' : wutils.SHOW_IF_TRUE, + 'usesqform' : wutils.SHOW_IF_TRUE, + 'displayinit' : wutils.SHOW_IF_TRUE, + 'noresample' : wutils.SHOW_IF_TRUE, + 'forcescaling' : wutils.SHOW_IF_TRUE, + 'applyxfm' : wutils.SHOW_IF_TRUE, + 'nosearch' : wutils.SHOW_IF_TRUE, + 'noclamp' : wutils.SHOW_IF_TRUE, + 'noresampblur' : wutils.SHOW_IF_TRUE, + '2D' : wutils.SHOW_IF_TRUE, + 'v' : wutils.SHOW_IF_TRUE } cmd = ['standard_space_roi', input, output] - - cmd += wutils.applyArgStyle('-', valmap=valmap, **kwargs) + cmd += wutils.applyArgStyle('-', argmap=argmap, valmap=valmap, **kwargs) return cmd