@@ -305,35 +305,60 @@ def _list_outputs(self):
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class EddyInputSpec ( FSLCommandInputSpec ):
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- in_file = File (exists = True , mandatory = True , desc = 'File containing all the images to estimate distortions for' , argstr = '--imain=%s' )
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- in_mask = File (exists = True , mandatory = True , desc = 'Mask to indicate brain' , argstr = '--mask=%s' )
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- in_index = File (exists = True , mandatory = True , desc = 'File containing indices for all volumes in --imain into --acqp and --topup' , argstr = '--index=%s' )
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- in_acqp = File (exists = True , mandatory = True , desc = 'File containing acquisition parameters' , argstr = '--acqp=%s' )
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- in_bvec = File (exists = True , mandatory = True , desc = 'File containing the b-vectors for all volumes in --imain' , argstr = '--bvecs=%s' )
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- in_bval = File (exists = True , mandatory = True , desc = 'File containing the b-values for all volumes in --imain' , argstr = '--bvals=%s' )
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-
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- out_base = File ( desc = 'basename for output (warped) image' , argstr = '--out=%s' )
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-
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-
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- session = File (exists = True , desc = 'File containing session indices for all volumes in --imain' , argstr = '--session=%s' )
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- in_topup_fieldcoef = File (exists = True , argstr = "--topup=%s" , requires = ['in_topup_movpar' ],
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- desc = 'topup file containing the field coefficients' )
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+ in_file = File (exists = True , mandatory = True ,
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+ desc = ('File containing all the images to estimate '
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+ 'distortions for' ), argstr = '--imain=%s' )
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+ in_mask = File (exists = True , mandatory = True ,
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+ desc = 'Mask to indicate brain' , argstr = '--mask=%s' )
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+ in_index = File (exists = True , mandatory = True ,
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+ desc = ('File containing indices for all volumes in --imain '
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+ 'into --acqp and --topup' ), argstr = '--index=%s' )
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+ in_acqp = File (exists = True , mandatory = True ,
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+ desc = 'File containing acquisition parameters' ,
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+ argstr = '--acqp=%s' )
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+ in_bvec = File (exists = True , mandatory = True ,
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+ desc = ('File containing the b-vectors for all volumes in '
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+ '--imain' ), argstr = '--bvecs=%s' )
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+ in_bval = File (exists = True , mandatory = True ,
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+ desc = ('File containing the b-values for all volumes in '
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+ '--imain' ), argstr = '--bvals=%s' )
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+ out_base = File ( desc = 'basename for output (warped) image' ,
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+ argstr = '--out=%s' )
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+ session = File (exists = True ,
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+ desc = ('File containing session indices for all volumes in '
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+ '--imain' ), argstr = '--session=%s' )
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+ in_topup_fieldcoef = File (exists = True , argstr = "--topup=%s" , copyfile = False ,
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+ requires = ['in_topup_movpar' ],
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+ desc = ('topup file containing the field '
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+ 'coefficients' ))
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in_topup_movpar = File (exists = True , requires = ['in_topup_fieldcoef' ],
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- desc = 'topup movpar.txt file' )
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- flm = traits .Enum ( ('linear' ,'quadratic' ,'cubic' ), desc = 'First level EC model' , argstr = '--flm=%s' )
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- fwhm = traits .Float ( desc = 'FWHM for conditioning filter when estimating the parameters' , argstr = '--fwhm=%s' )
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- niter = traits .Int ( 5 , desc = 'Number of iterations' , argstr = '--niter=%s' )
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- method = traits .Enum ( ('jac' ,'lsr' ), argstr = '--resamp=%s' , desc = 'Final resampling method (jacobian/least squeares)' )
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- repol = traits .Bool ( False , desc = 'Detect and replace outlier slices' , argstr = '--repol' )
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+ copyfile = False , desc = 'topup movpar.txt file' )
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+ flm = traits .Enum (('linear' ,'quadratic' ,'cubic' ),
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+ desc = 'First level EC model' , argstr = '--flm=%s' )
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+ fwhm = traits .Float (desc = ('FWHM for conditioning filter when estimating '
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+ 'the parameters' ), argstr = '--fwhm=%s' )
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+ niter = traits .Int ( 5 , desc = 'Number of iterations' , argstr = '--niter=%s' )
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+ method = traits .Enum (('jac' ,'lsr' ), argstr = '--resamp=%s' ,
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+ desc = ('Final resampling method (jacobian/least '
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+ 'squeares)' ))
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+ repol = traits .Bool ( False , desc = 'Detect and replace outlier slices' ,
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+ argstr = '--repol' )
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+
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class EddyOutputSpec ( TraitedSpec ):
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- out_corrected = File ( exists = True , desc = '4D image file containing all the corrected volumes' )
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- out_parameter = File ( exists = True , desc = 'text file with parameters definining the field and movement for each scan' )
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+ out_corrected = File (exists = True ,
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+ desc = ('4D image file containing all the corrected '
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+ 'volumes' ))
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+ out_parameter = File (exists = True ,
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+ desc = ('text file with parameters definining the field '
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+ 'and movement for each scan' ))
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class Eddy ( FSLCommand ):
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- """ Interface for FSL eddy, a tool for estimating and correcting eddy currents induced distortions.
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- `User guide <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Eddy/UsersGuide>`_ and
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- `more info regarding acqp file <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/Faq#How_do_I_know_what_to_put_into_my_--acqp_file>`_.
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+ """ Interface for FSL eddy, a tool for estimating and correcting eddy
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+ currents induced distortions. `User guide
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+ <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Eddy/UsersGuide>`_ and
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+ `more info regarding acqp file
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+ <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/Faq#How_do_I_know_what_to_put_into_my_--acqp_file>`_.
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Examples
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--------
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