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# interfaces.fsl.possum

## B0Calc

Link to code

Wraps 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 --b0=3.00'

Inputs:

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

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    chi_air: (a float)
            susceptibility of air
            flag: --chi0=%e
    compute_xyz: (a boolean)
            calculate and save all 3 field components (i.e. x,y,z)
            flag: --xyz
    delta: (a float)
            Delta value (chi_tissue - chi_air)
            flag: -d %e
    directconv: (a boolean)
            use direct (image space) convolution, not FFT
            flag: --directconv
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    extendboundary: (a float)
            Relative proportion to extend voxels at boundary
            flag: --extendboundary=%0.2f
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    out_file: (a file name)
            filename of B0 output volume
            flag: -o %s, position: 1
    output_type: (u'NIFTI_PAIR' or u'NIFTI_PAIR_GZ' or u'NIFTI_GZ' or
             u'NIFTI')
            FSL output type
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    x_b0: (a float)
            Value for zeroth-order b0 field (x-component), in Tesla
            flag: --b0x=%0.2f
            mutually_exclusive: xyz_b0
    x_grad: (a float)
            Value for zeroth-order x-gradient field (per mm)
            flag: --gx=%0.4f
    xyz_b0: (a tuple of the form: (a float, a float, a float))
            Zeroth-order B0 field in Tesla
            flag: --b0x=%0.2f --b0y=%0.2f --b0=%0.2f
            mutually_exclusive: x_b0, y_b0, z_b0
    y_b0: (a float)
            Value for zeroth-order b0 field (y-component), in Tesla
            flag: --b0y=%0.2f
            mutually_exclusive: xyz_b0
    y_grad: (a float)
            Value for zeroth-order y-gradient field (per mm)
            flag: --gy=%0.4f
    z_b0: (a float)
            Value for zeroth-order b0 field (z-component), in Tesla
            flag: --b0=%0.2f
            mutually_exclusive: xyz_b0
    z_grad: (a float)
            Value for zeroth-order z-gradient field (per mm)
            flag: --gz=%0.4f

Outputs:

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

References:: None