interfaces.fsl.possum¶
B0Calc¶
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]
directconv: (a boolean, nipype default value: False)
use direct (image space) convolution, not FFT
argument: ``--directconv``
extendboundary: (a float, nipype default value: 1.0)
Relative proportion to extend voxels at boundary
argument: ``--extendboundary=%0.2f``
out_file: (a file name)
filename of B0 output volume
argument: ``-o %s``, position: 1
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
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
delta: (a float, nipype default value: -9.45e-06)
Delta value (chi_tissue - chi_air)
argument: ``-d %e``
x_grad: (a float, nipype default value: 0.0)
Value for zeroth-order x-gradient field (per mm)
argument: ``--gx=%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
compute_xyz: (a boolean, nipype default value: False)
calculate and save all 3 field components (i.e. x,y,z)
argument: ``--xyz``
z_grad: (a float, nipype default value: 0.0)
Value for zeroth-order z-gradient field (per mm)
argument: ``--gz=%0.4f``
chi_air: (a float, nipype default value: 4e-07)
susceptibility of air
argument: ``--chi0=%e``
y_grad: (a float, nipype default value: 0.0)
Value for zeroth-order y-gradient field (per mm)
argument: ``--gy=%0.4f``
output_type: ('NIFTI_PAIR_GZ' or 'NIFTI_GZ' or 'NIFTI' or
'NIFTI_PAIR')
FSL output type
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
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
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
Outputs:
out_file: (an existing file name)
filename of B0 output volume
References:¶
None