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Added interface for topup
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‎nipype/interfaces/fsl/epi.py‎

Lines changed: 89 additions & 64 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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"""The fsl module provides classes for interfacing with the `FSL
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<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
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was written to work with FSL version 4.1.4.
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was written to work with FSL version 5.0.4.
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Examples
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--------
@@ -45,7 +45,7 @@ class PrepareFieldmapOutputSpec( TraitedSpec ):
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out_fieldmap = File( exists=True, desc='output name for prepared fieldmap' )
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class PrepareFieldmap(FSLCommand):
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""" Interface for the fsl_prepare_fieldmap script
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""" Interface for the fsl_prepare_fieldmap script (FSL 5.0)
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Prepares a fieldmap suitable for FEAT from SIEMENS data - saves output in rad/s format
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e.g. fsl_prepare_fieldmap SIEMENS images_3_gre_field_mapping images_4_gre_field_mapping fmap_rads 2.65
@@ -84,75 +84,100 @@ def _list_outputs(self):
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# class TOPUPInputSpec( FSLCommandInputSpec ):
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# in_file = File( exists=True, mandatory=True, desc='name of 4D file with images', argstr='--imain %s' )
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# encoding_file = File( exists=True, mandatory=True, desc='name of text file with PE directions/times', argstr='--datain %s' )
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# out_base = File( desc='base-name of output files (spline coefficients (Hz) and movement parameters)', argstr='--out %s' )
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# out_field = File( argstr='--fout %s', desc='name of image file with field (Hz)' )
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# out_corrected = File( argstr='--iout %s', desc='name of 4D image file with unwarped images' )
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# out_logfile = File( argstr='--logout %s', desc='name of log-file' )
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# warp_res = traits.Float( 10.0, argstr='--warpres %f', desc='(approximate) resolution (in mm) of warp basis for the different sub-sampling levels' )
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# subsamp = traits.Int( 1, argstr='--subsamp %d', desc='sub-sampling scheme, default 1' )
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# fwhm = traits.Float( 8.0, argstr='--fwhm %f', desc='FWHM (in mm) of gaussian smoothing kernel' )
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# config = File( desc='Name of config file specifying command line arguments', argstr='--config %s' )
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# max_iter = traits.Int( 5, argstr='--miter %d', desc='max # of non-linear iterations')
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# #lambda Weight of regularisation, default depending on --ssqlambda and --regmod switches. See user documetation.
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# #ssqlambda If set (=1), lambda is weighted by current ssq, default 1
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# #regmod Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy
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# estmov = traits.Either( (0,1), desc='estimate movements if set', argstr='--estmov %d' )
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# minmet = traits.Either( (0,1), desc='Minimisation method 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient', argstr='--minmet %d' )
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# splineorder = traits.Int( 3, argstr='--splineorder %d', desc='order of spline, 2->Qadratic spline, 3->Cubic spline' )
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# numprec = traits.Either( ('float','double'), argstr='--numprec %s', desc='Precision for representing Hessian, double or float.' )
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# interp = traits.Either( ('linear','spline'), argstr='--interp %s', desc='Image interpolation model, linear or spline.' )
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# scale = traits.Either( (0,1), argstr='--scale %d', desc='If set (=1), the images are individually scaled to a common mean' )
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# regrid = traits.Either( (0,1), argstr='--regrid %d', desc='If set (=1), the calculations are done in a different grid' )
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#
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#
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#
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# class TOPUPOutputSpec( TraitedSpec ):
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# out_field = File( argstr='--fout %s', desc='name of image file with field (Hz)' )
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# out_corrected = File( argstr='--iout %s', desc='name of 4D image file with unwarped images' )
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# out_logfile = File( argstr='--logout %s', desc='name of log-file' )
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#
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#
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#
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# class TOPUP( FSLCommand ):
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# """ Interface for FSL topup, a tool for estimating and correcting susceptibility induced distortions
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# Reference: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP
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# Example: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup
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#
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# topup --imain=<some 4D image> --datain=<text file> --config=<text file with parameters> --coutname=my_field
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#
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#
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# Examples
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# --------
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# >>> topup = TOPUP()
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# >>> topup.inputs.in_file = "dwi_combined.nii"
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# >>> topup.inputs.encoding_file = "encoding.txt"
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# >>> res = topup.run() # doctest: +SKIP
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#
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# """
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# _cmd = 'topup'
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# input_spec = TOPUPInputSpec
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# output_spec = TOPUPOutputSpec
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#
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# def _list_outputs(self):
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# outputs = self.output_spec().get()
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#
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# return outputs
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#
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#
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#
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class TOPUPInputSpec( FSLCommandInputSpec ):
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in_file = File( exists=True, mandatory=True, desc='name of 4D file with images', argstr='--imain %s' )
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encoding_file = File( exists=True, mandatory=True, desc='name of text file with PE directions/times', argstr='--datain %s' )
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out_base = File( desc='base-name of output files (spline coefficients (Hz) and movement parameters)', argstr='--out %s' )
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out_field = File( argstr='--fout %s', desc='name of image file with field (Hz)' )
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out_corrected = File( argstr='--iout %s', desc='name of 4D image file with unwarped images' )
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out_logfile = File( argstr='--logout %s', desc='name of log-file' )
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warp_res = traits.Float( 10.0, argstr='--warpres %f', desc='(approximate) resolution (in mm) of warp basis for the different sub-sampling levels' )
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subsamp = traits.Int( 1, argstr='--subsamp %d', desc='sub-sampling scheme, default 1' )
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fwhm = traits.Float( 8.0, argstr='--fwhm %f', desc='FWHM (in mm) of gaussian smoothing kernel' )
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config = traits.String('b02b0.cnf' desc='Name of config file specifying command line arguments', argstr='--config %s' )
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max_iter = traits.Int( 5, argstr='--miter %d', desc='max # of non-linear iterations')
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#lambda Weight of regularisation, default depending on --ssqlambda and --regmod switches. See user documetation.
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#ssqlambda If set (=1), lambda is weighted by current ssq, default 1
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#regmod Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy
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estmov = traits.Enum( 1, 0, desc='estimate movements if set', argstr='--estmov %d' )
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minmet = traits.Enum( 0, 1, desc='Minimisation method 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient', argstr='--minmet %d' )
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splineorder = traits.Int( 3, argstr='--splineorder %d', desc='order of spline, 2->Qadratic spline, 3->Cubic spline' )
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numprec = traits.Enum( 'double', 'float', argstr='--numprec %s', desc='Precision for representing Hessian, double or float.' )
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interp = traits.Enum( 'spline', 'linear' , argstr='--interp %s', desc='Image interpolation model, linear or spline.' )
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scale = traits.Enum( 0, 1, argstr='--scale %d', desc='If set (=1), the images are individually scaled to a common mean' )
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regrid = traits.Enum( 1, 0, argstr='--regrid %d', desc='If set (=1), the calculations are done in a different grid' )
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class TOPUPOutputSpec( TraitedSpec ):
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out_field = File( exists=True, desc='file containing the field coefficients' )
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out_movpar = File( exists=True, desc='movpar.txt output file' )
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out_topup = File( desc='basename for the <out_base>_fieldcoef.nii.gz and <out_base>_movpar.txt files' )
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out_field = File( desc='name of image file with field (Hz)' )
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out_corrected = File( desc='name of 4D image file with unwarped images' )
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out_logfile = File( desc='name of log-file' )
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class TOPUP( FSLCommand ):
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""" Interface for FSL topup, a tool for estimating and correcting susceptibility induced distortions
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Reference: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP
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Example: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup
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topup --imain=<some 4D image> --datain=<text file> --config=<text file with parameters> --coutname=my_field
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Examples
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--------
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>>> topup = TOPUP()
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>>> topup.inputs.in_file = "b0_b0rev.nii"
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>>> topup.inputs.encoding_file = "encoding.txt"
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>>> res = topup.run() # doctest: +SKIP
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"""
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_cmd = 'topup'
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input_spec = TOPUPInputSpec
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output_spec = TOPUPOutputSpec
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def _parse_inputs( self, skip=None ):
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if skip is None:
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skip = []
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if not isdefined(self.inputs.out_base ):
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self.inputs.out_base = os.path.abspath( './nipype_topup' )
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return super(TOPUP, self)._parse_inputs(skip=skip)
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def _list_outputs(self):
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outputs = self.output_spec().get()
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outputs['out_topup'] = self.inputs.out_base
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outputs['out_field'] = '%s_%s.nii.gz' % (self.inputs.out_base, 'fieldcoef' )
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outputs['out_movpar'] = '%s_%s.txt' % (self.inputs.out_base, 'movpar' )
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if isdefined( self.inputs.out_field ):
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outputs['out_field'] = self.inputs.out_field
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else:
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outputs['out_field'] = None
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if isdefined( self.inputs.out_corrected ):
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outputs['out_corrected'] = self.inputs.out_corrected
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else:
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outputs['out_corrected'] = None
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if isdefined( self.inputs.out_logfile ):
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outputs['out_logfile'] = self.inputs.out_logfile
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else:
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outputs['out_logfile'] = None
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return outputs
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# class ApplyTOPUPInputSpec( FSLCommandInputSpec ):
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# in_file = File( exists=True, mandatory=True, desc='name of 4D file with images', argstr='--imain %s' )
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# encoding_file = File( exists=True, mandatory=True, desc='name of text file with PE directions/times', argstr='--datain %s' )
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# in_index = traits.List( argstr='-x %s', mandatory=True, desc='comma separated list of indicies into --datain of the input image (to be corrected)' )
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# in_topup = File( mandatory=True, desc='basename of field/movements (from topup)', argstr='-t %s' )
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#
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# out_base = File( desc='basename for output (warped) image', argstr='-o %s' )
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# method = traits.Either( ('jac','lsr'), argstr='-m %s', desc='use jacobian modulation (jac) or least-squares resampling (lsr)' )
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# interp = traits.Either( ('trilinear','spline'), argstr='-n %s', desc='interpolation method' )
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# datatype = traits.Either( ('char', 'short', 'int', 'float', 'double' ), argstr='-d %s', desc='force output data type' )
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# method = traits.Enum( ('jac','lsr'), argstr='-m %s', desc='use jacobian modulation (jac) or least-squares resampling (lsr)' )
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# interp = traits.Enum( ('trilinear','spline'), argstr='-n %s', desc='interpolation method' )
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# datatype = traits.Enum( ('char', 'short', 'int', 'float', 'double' ), argstr='-d %s', desc='force output data type' )
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#
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#
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# class ApplyTOPUPOutputSpec( TraitedSpec ):

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