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.. Note:: This was written to work with FSL version 5.0.6.
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.. testsetup::
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-
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# Change directory to provide relative paths for doctests
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import os
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filepath = os.path.dirname( os.path.realpath( __file__ ) )
@@ -30,32 +29,33 @@ class B0CalcInputSpec(FSLCommandInputSpec):
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name_template = '%s_b0field' , output_name = 'out_file' ,
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desc = 'filename of B0 output volume' )
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+ x_grad = traits .Float (0.0 , argstr = '--gx=%0.4f' ,
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+ desc = 'Value for zeroth-order x-gradient field (per mm)' )
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+ y_grad = traits .Float (0.0 , argstr = '--gy=%0.4f' ,
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+ desc = 'Value for zeroth-order y-gradient field (per mm)' )
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+ z_grad = traits .Float (0.0 , argstr = '--gz=%0.4f' ,
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+ desc = 'Value for zeroth-order z-gradient field (per mm)' )
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- x_grad = traits .Float (0.0 , argstr = '--gx=%0.4f' , desc = ('Value for zeroth-order x-gradient field '
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- '(per mm)' ))
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- y_grad = traits .Float (0.0 , argstr = '--gy=%0.4f' , desc = ('Value for zeroth-order y-gradient field '
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- '(per mm)' ))
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- z_grad = traits .Float (0.0 , argstr = '--gz=%0.4f' , desc = ('Value for zeroth-order z-gradient field '
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- '(per mm)' ))
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-
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- x_b0 = traits .Float (0.0 , argstr = '--b0x=%0.2f' , desc = ('Value for zeroth-order b0 field '
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- '(x-component), in Tesla' ), xor = ['xyz_b0' ])
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- y_b0 = traits .Float (0.0 , argstr = '--b0y=%0.2f' , desc = ('Value for zeroth-order b0 field '
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- '(y-component), in Tesla' ), xor = ['xyz_b0' ])
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- z_b0 = traits .Float (1.0 , argstr = '--b0=%0.2f' , desc = ('Value for zeroth-order b0 field '
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- '(z-component), in Tesla' ), xor = ['xyz_b0' ])
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+ x_b0 = traits .Float (0.0 , argstr = '--b0x=%0.2f' , xor = ['xyz_b0' ],
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+ desc = 'Value for zeroth-order b0 field (x-component), in Tesla' )
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+ y_b0 = traits .Float (0.0 , argstr = '--b0y=%0.2f' , xor = ['xyz_b0' ],
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+ desc = 'Value for zeroth-order b0 field (y-component), in Tesla' )
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+ z_b0 = traits .Float (1.0 , argstr = '--b0=%0.2f' , xor = ['xyz_b0' ],
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+ desc = 'Value for zeroth-order b0 field (z-component), in Tesla' )
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xyz_b0 = traits .Tuple (
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traits .Float , traits .Float , traits .Float ,
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- argstr = '--b0x=%0.2f --b0y=%0.2f --b0=%0.2f' , xor = ['x_b0' ,'y_b0' ,'z_b0' ],
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+ argstr = '--b0x=%0.2f --b0y=%0.2f --b0=%0.2f' , xor = ['x_b0' , 'y_b0' , 'z_b0' ],
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desc = 'Zeroth-order B0 field in Tesla' )
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- delta = traits .Float (- 9.45e-6 , argstr = '-d %e' , desc = 'Delta value (chi_tissue - chi_air)' )
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- chi_air = traits .Float (4.0e-7 , argstr = '--chi0=%e' , desc = 'susceptibility of air' )
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+ delta = traits .Float (- 9.45e-6 , argstr = '-d %e' ,
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+ desc = 'Delta value (chi_tissue - chi_air)' )
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+ chi_air = traits .Float (
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+ 4.0e-7 , argstr = '--chi0=%e' , desc = 'susceptibility of air' )
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compute_xyz = traits .Bool (False , argstr = '--xyz' ,
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desc = 'calculate and save all 3 field components (i.e. x,y,z)' )
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- extendboundary = traits .Float (1.0 , argstr = '--extendboundary=%0.2f' , desc = ( 'Relative proportion to '
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- ' extend voxels at boundary') )
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+ extendboundary = traits .Float (1.0 , argstr = '--extendboundary=%0.2f' ,
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+ desc = 'Relative proportion to extend voxels at boundary' )
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directconv = traits .Bool (False , argstr = '--directconv' ,
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desc = 'use direct (image space) convolution, not FFT' )
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@@ -65,13 +65,15 @@ class B0CalcOutputSpec(TraitedSpec):
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class B0Calc (FSLCommand ):
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+
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"""
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B0 inhomogeneities occur at interfaces of materials with different magnetic susceptibilities,
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such as tissue-air interfaces. These differences lead to distortion in the local magnetic field,
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as Maxwell’s equations need to be satisfied. An example of B0 inhomogneity is the first volume
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of the 4D volume ```$FSLDIR/data/possum/b0_ppm.nii.gz```.
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- Examples ::
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+ Examples
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+ --------
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>>> from nipype.interfaces.fsl import B0Calc
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>>> b0calc = B0Calc()
@@ -85,5 +87,3 @@ class B0Calc(FSLCommand):
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_cmd = 'b0calc'
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input_spec = B0CalcInputSpec
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output_spec = B0CalcOutputSpec
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-
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-
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