Base files for new epi interfaces

Added base classes for interfaces fsl_prepare_fieldmap, topup and applytopup

Author: oesteban

nipype/interfaces/fsl/epi.py

@@ -25,6 +25,154 @@
 warnings.filterwarnings('always', category=UserWarning)
 
 
+class PrepareFieldmapInputSpec(FSLCommandInputSpec):
+ scanner = traits.String('SIEMENS', desc='must be SIEMENS', position=0, usedefault=True)
+ in_phase = File( exists=True, desc='Phase difference map, in SIEMENS format range from 0-4096 or 0-8192 )',
+ position=1, mandatory=True )
+ in_magnitude = File(exists=True, 
+ position=2, 
+ desc='Magnitude difference map, brain extracted',
+ mandatory=True
+ )
+ out_fieldmap = File()
+ delta_TE = traits.Float(2.46,desc='echo time difference of the fielmap sequence in ms. (usually 2.46ms in Siemens)',
+ usedefault=True )
+ nocheck = traits.Bool(False,desc='do not perform sanity checks for image size/range/dimensions',
+ argstr='--nocheck' )
+
+class PrepareFieldmapOutputSpec( FSLCommandOutputSpec ):
+ out_fieldmap = File( exists=True )
+
+class PrepareFieldmap(FSLCommand):
+ """ Interface for the fsl_prepare_fielmap script
+
+ Prepares a fieldmap suitable for FEAT from SIEMENS data - saves output in rad/s format
+ e.g. fsl_prepare_fieldmap SIEMENS images_3_gre_field_mapping images_4_gre_field_mapping fmap_rads 2.65
+
+
+ Examples
+ --------
+ >>> prepare = PrepareFieldmap()
+ >>> prepare.inputs.in_phase = "phase.nii"
+ >>> prepare.inputs.in_magnitude = "magnitude.nii"
+ >>> res = prepare.run() # doctest: +SKIP
+
+
+ """
+ _cmd = 'fsl_prepare_fieldmap'
+ input_spec = PrepareFieldmapInputSpec
+ output_spec = PrepareFieldmapOutputSpec
+
+ def _list_outputs(self):
+ outputs = self.output_spec().get()
+
+ return outputs
+
+
+class TOPUPInputSpec( FSLCommandInputSpec ):
+in_file = File( exists=True, mandatory=True, desc='name of 4D file with images', argstr='--imain %s' )
+encoding_file = File( exists=True, mandatory=True, desc='name of text file with PE directions/times', argstr='--datain %s' )
+out_base = File( desc='base-name of output files (spline coefficients (Hz) and movement parameters)', argstr='--out %s' )
+ out_field = File( argstr='--fout %s', desc='name of image file with field (Hz)' )
+ out_corrected = File( argstr='--iout %s', desc='name of 4D image file with unwarped images' )
+ out_logfile = File( argstr='--logout %s', desc='name of log-file' )
+ warp_res = traits.Float( 10.0, argstr='--warpres %f', desc='(approximate) resolution (in mm) of warp basis for the different sub-sampling levels' )
+ subsamp = traits.Int( 1, argstr='--subsamp %d', desc='sub-sampling scheme, default 1' )
+ fwhm = traits.Float( 8.0, argstr='--fwhm %f', desc='FWHM (in mm) of gaussian smoothing kernel' )
+config = File( desc='Name of config file specifying command line arguments', argstr='--config %s' )
+ max_iter = traits.Int( 5, argstr='--miter %d', desc='max # of non-linear iterations')
+ #lambda	Weight of regularisation, default depending on --ssqlambda and --regmod switches. See user documetation.
+#ssqlambda	If set (=1), lambda is weighted by current ssq, default 1
+#regmod	Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy
+estmov = traits.Either( (0,1), desc='estimate movements if set', argstr='--estmov %d' )
+ minmet = traits.Either( (0,1), desc='Minimisation method 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient', argstr='--minmet %d' )
+splineorder = traits.Int( 3, argstr='--splineorder %d', desc='order of spline, 2->Qadratic spline, 3->Cubic spline' )
+ numprec = traits.Either( ('float','double'), argstr='--numprec %s', desc='Precision for representing Hessian, double or float.' )
+ interp = traits.Either( ('linear','spline'), argstr='--interp %s', desc='Image interpolation model, linear or spline.' )
+ scale = traits.Either( (0,1), argstr='--scale %d', desc='If set (=1), the images are individually scaled to a common mean' )
+ regrid = traits.Either( (0,1), argstr='--regrid %d', desc='If set (=1), the calculations are done in a different grid' )
+
+
+
+class TOPUPOutputSpec( FSLCommandOutputSpec ):
+ out_field = File( argstr='--fout %s', desc='name of image file with field (Hz)' )
+ out_corrected = File( argstr='--iout %s', desc='name of 4D image file with unwarped images' )
+ out_logfile = File( argstr='--logout %s', desc='name of log-file' )
+
+
+
+class TOPUP( FSLCommand ):
+ """ Interface for FSL topup, a tool for estimating and correcting susceptibility induced distortions
+ Reference: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP
+ Example: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup
+
+ topup --imain=<some 4D image> --datain=<text file> --config=<text file with parameters> --coutname=my_field
+
+
+ Examples
+ --------
+ >>> topup = TOPUP()
+ >>> topup.inputs.in_file = "dwi_combined.nii"
+ >>> topup.inputs.encoding_file = "encoding.txt"
+ >>> res = topup.run() # doctest: +SKIP
+
+ """
+ _cmd = 'topup'
+ input_spec = TOPUPInputSpec
+ output_spec = TOPUPOutputSpec
+
+ def _list_outputs(self):
+ outputs = self.output_spec().get()
+
+ return outputs
+
+
+
+class ApplyTOPUPInputSpec( FSLCommandInputSpec ):
+in_file = File( exists=True, mandatory=True, desc='name of 4D file with images', argstr='--imain %s' )
+encoding_file = File( exists=True, mandatory=True, desc='name of text file with PE directions/times', argstr='--datain %s' )
+ in_index = traits.List( argstr='-x %s', mandatory=True, desc='comma separated list of indicies into --datain of the input image (to be corrected)' )
+ in_topup = File( mandatory=True, desc='basename of field/movements (from topup)', argstr='-t %s' )
+ 
+ out_base = File( desc='basename for output (warped) image', argstr='-o %s' )
+ method = traits.Either( ('jac','lsr'), argstr='-m %s', desc='use jacobian modulation (jac) or least-squares resampling (lsr)' )
+ interp = traits.Either( ('trilinear','spline'), argstr='-n %s', desc='interpolation method' )
+ datatype = traits.Either( ('char', 'short', 'int', 'float', 'double' ), argstr='-d %s', desc='force output data type' )
+
+
+class ApplyTOPUPOutputSpec( FSLCommandOutputSpec ):
+ out_corrected = File( argstr='--iout %s', desc='name of 4D image file with unwarped images' )
+ out_logfile = File( argstr='--logout %s', desc='name of log-file' )
+
+class ApplyTOPUP( FSLCommand ):
+ """ Interface for FSL topup, a tool for estimating and correcting susceptibility induced distortions
+ Reference: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ApplytopupUsersGuide
+ Example: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup
+
+ topup --imain=<some 4D image> --datain=<text file> --config=<text file with parameters> --coutname=my_field
+
+
+ Examples
+ --------
+ >>> applytopup = ApplyTOPUP()
+ >>> applytopup.inputs.in_file = "dwi_combined.nii"
+ >>> applytopup.inputs.encoding_file = "encoding.txt"
+ >>> applytopup.inputs.in_index = 1,2
+ >>> applytopup.inputs.in_topup = "my_topup_results"
+ >>> res = applytopup.run() # doctest: +SKIP
+
+ """
+ _cmd = 'topup'
+ input_spec = ApplyTOPUPInputSpec
+ output_spec = ApplyTOPUPOutputSpec
+
+ def _list_outputs(self):
+ outputs = self.output_spec().get()
+
+ return outputs
+
+
+