interfaces.fsl.possum

B0Calc

Link to code

Wraps the executable command b0calc.

B0 inhomogeneities occur at interfaces of materials with different magnetic susceptibilities, such as tissue-air interfaces. These differences lead to distortion in the local magnetic field, as Maxwell’s equations need to be satisfied. An example of B0 inhomogneity is the first volume of the 4D volume `$FSLDIR/data/possum/b0_ppm.nii.gz`.

Examples

>>> from nipype.interfaces.fsl import B0Calc
>>> b0calc = B0Calc()
>>> b0calc.inputs.in_file = 'tissue+air_map.nii'
>>> b0calc.inputs.z_b0 = 3.0
>>> b0calc.inputs.output_type = "NIFTI_GZ"
>>> b0calc.cmdline
'b0calc -i tissue+air_map.nii -o tissue+air_map_b0field.nii.gz --chi0=4.000000e-07 -d -9.450000e-06 --extendboundary=1.00 --b0x=0.00 --gx=0.0000 --b0y=0.00 --gy=0.0000 --b0=3.00 --gz=0.0000'

Inputs:

[Mandatory]
in_file: (an existing file name)
        filename of input image (usually a tissue/air segmentation)
        argument: ``-i %s``, position: 0

[Optional]
out_file: (a file name)
        filename of B0 output volume
        argument: ``-o %s``, position: 1
x_grad: (a float, nipype default value: 0.0)
        Value for zeroth-order x-gradient field (per mm)
        argument: ``--gx=%0.4f``
y_grad: (a float, nipype default value: 0.0)
        Value for zeroth-order y-gradient field (per mm)
        argument: ``--gy=%0.4f``
z_grad: (a float, nipype default value: 0.0)
        Value for zeroth-order z-gradient field (per mm)
        argument: ``--gz=%0.4f``
x_b0: (a float, nipype default value: 0.0)
        Value for zeroth-order b0 field (x-component), in Tesla
        argument: ``--b0x=%0.2f``
        mutually_exclusive: xyz_b0
y_b0: (a float, nipype default value: 0.0)
        Value for zeroth-order b0 field (y-component), in Tesla
        argument: ``--b0y=%0.2f``
        mutually_exclusive: xyz_b0
z_b0: (a float, nipype default value: 1.0)
        Value for zeroth-order b0 field (z-component), in Tesla
        argument: ``--b0=%0.2f``
        mutually_exclusive: xyz_b0
xyz_b0: (a tuple of the form: (a float, a float, a float))
        Zeroth-order B0 field in Tesla
        argument: ``--b0x=%0.2f --b0y=%0.2f --b0=%0.2f``
        mutually_exclusive: x_b0, y_b0, z_b0
delta: (a float, nipype default value: -9.45e-06)
        Delta value (chi_tissue - chi_air)
        argument: ``-d %e``
chi_air: (a float, nipype default value: 4e-07)
        susceptibility of air
        argument: ``--chi0=%e``
compute_xyz: (a boolean, nipype default value: False)
        calculate and save all 3 field components (i.e. x,y,z)
        argument: ``--xyz``
extendboundary: (a float, nipype default value: 1.0)
        Relative proportion to extend voxels at boundary
        argument: ``--extendboundary=%0.2f``
directconv: (a boolean, nipype default value: False)
        use direct (image space) convolution, not FFT
        argument: ``--directconv``
output_type: ('NIFTI' or 'NIFTI_PAIR' or 'NIFTI_GZ' or
          'NIFTI_PAIR_GZ')
        FSL output type
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
          of class 'str' and with values which are a bytes or None or a
          value of class 'str', nipype default value: {})
        Environment variables

Outputs:

out_file: (an existing file name)
        filename of B0 output volume

References:

None