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 --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)
        flag: -i %s, position: 0

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
chi_air: (a float, nipype default value: 4e-07)
        susceptibility of air
        flag: --chi0=%e
compute_xyz: (a boolean, nipype default value: False)
        calculate and save all 3 field components (i.e. x,y,z)
        flag: --xyz
delta: (a float, nipype default value: -9.45e-06)
        Delta value (chi_tissue - chi_air)
        flag: -d %e
directconv: (a boolean, nipype default value: False)
        use direct (image space) convolution, not FFT
        flag: --directconv
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
extendboundary: (a float, nipype default value: 1.0)
        Relative proportion to extend voxels at boundary
        flag: --extendboundary=%0.2f
out_file: (a file name)
        filename of B0 output volume
        flag: -o %s, position: 1
output_type: ('NIFTI' or 'NIFTI_PAIR' or 'NIFTI_GZ' or
         'NIFTI_PAIR_GZ')
        FSL output type
x_b0: (a float, nipype default value: 0.0)
        Value for zeroth-order b0 field (x-component), in Tesla
        flag: --b0x=%0.2f
        mutually_exclusive: xyz_b0
x_grad: (a float, nipype default value: 0.0)
        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, nipype default value: 0.0)
        Value for zeroth-order b0 field (y-component), in Tesla
        flag: --b0y=%0.2f
        mutually_exclusive: xyz_b0
y_grad: (a float, nipype default value: 0.0)
        Value for zeroth-order y-gradient field (per mm)
        flag: --gy=%0.4f
z_b0: (a float, nipype default value: 1.0)
        Value for zeroth-order b0 field (z-component), in Tesla
        flag: --b0=%0.2f
        mutually_exclusive: xyz_b0
z_grad: (a float, nipype default value: 0.0)
        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:: BibTeX(‘@article{JenkinsonBeckmannBehrensWoolrichSmith2012,author={M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, and S.M. Smith},title={FSL},journal={NeuroImage},volume={62},pages={782-790},year={2012},}’, key=’JenkinsonBeckmannBehrensWoolrichSmith2012’)