nipype.interfaces.petpvc module

PETPVC is a toolbox for partial volume correction in positron emission tomography.

class nipype.interfaces.petpvc.PETPVC(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: CommandLine

Wrapped executable: petpvc.

Use PETPVC for partial volume correction of PET images.

PETPVC ([1], [2]) is a software from the Nuclear Medicine Department of the UCL University Hospital, London, UK.

Examples

>>> from ..testing import example_data
>>> #TODO get data for PETPVC
>>> pvc = PETPVC()
>>> pvc.inputs.in_file   = 'pet.nii.gz'
>>> pvc.inputs.mask_file = 'tissues.nii.gz'
>>> pvc.inputs.out_file  = 'pet_pvc_rbv.nii.gz'
>>> pvc.inputs.pvc = 'RBV'
>>> pvc.inputs.fwhm_x = 2.0
>>> pvc.inputs.fwhm_y = 2.0
>>> pvc.inputs.fwhm_z = 2.0
>>> outs = pvc.run()

References

Mandatory Inputs:

  • fwhm_x (a float) – The full-width at half maximum in mm along x-axis. Maps to a command-line argument: -x %.4f.

  • fwhm_y (a float) – The full-width at half maximum in mm along y-axis. Maps to a command-line argument: -y %.4f.

  • fwhm_z (a float) – The full-width at half maximum in mm along z-axis. Maps to a command-line argument: -z %.4f.

  • in_file (a pathlike object or string representing an existing file) – PET image file. Maps to a command-line argument: -i %s.

  • mask_file (a pathlike object or string representing an existing file) – Mask image file. Maps to a command-line argument: -m %s.

  • pvc (‘GTM’ or ‘IY’ or ‘IY+RL’ or ‘IY+VC’ or ‘LABBE’ or ‘LABBE+MTC’ or ‘LABBE+MTC+RL’ or ‘LABBE+MTC+VC’ or ‘LABBE+RBV’ or ‘LABBE+RBV+RL’ or ‘LABBE+RBV+VC’ or ‘MG’ or ‘MG+RL’ or ‘MG+VC’ or ‘MTC’ or ‘MTC+RL’ or ‘MTC+VC’ or ‘RBV’ or ‘RBV+RL’ or ‘RBV+VC’ or ‘RL’ or ‘VC’ or ‘STC’) –

    Desired PVC method:

    • Geometric transfer matrix – GTM

    • Labbe approach – LABBE

    • Richardson-Lucy – RL

    • Van-Cittert – VC

    • Region-based voxel-wise correction – RBV

    • RBV with Labbe – LABBE+RBV

    • RBV with Van-Cittert – RBV+VC

    • RBV with Richardson-Lucy – RBV+RL

    • RBV with Labbe and Van-Cittert – LABBE+RBV+VC

    • RBV with Labbe and Richardson-Lucy – LABBE+RBV+RL

    • Multi-target correction – MTC

    • MTC with Labbe – LABBE+MTC

    • MTC with Van-Cittert – MTC+VC

    • MTC with Richardson-Lucy – MTC+RL

    • MTC with Labbe and Van-Cittert – LABBE+MTC+VC

    • MTC with Labbe and Richardson-Lucy – LABBE+MTC+RL

    • Iterative Yang – IY

    • Iterative Yang with Van-Cittert – IY+VC

    • Iterative Yang with Richardson-Lucy – IY+RL

    • Muller Gartner – MG

    • Muller Gartner with Van-Cittert – MG+VC

    • Muller Gartner with Richardson-Lucy – MG+RL

    • Single-target correction – STC

    Maps to a command-line argument: -p %s.

Optional Inputs:

  • alpha (a float) – Alpha value. Maps to a command-line argument: -a %.4f. (Nipype default value: 1.5)

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • debug (a boolean) – Prints debug information. Maps to a command-line argument: -d. (Nipype default value: False)

  • 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’) – Environment variables. (Nipype default value: {})

  • n_deconv (an integer) – Number of deconvolution iterations. Maps to a command-line argument: -k %d. (Nipype default value: 10)

  • n_iter (an integer) – Number of iterations. Maps to a command-line argument: -n %d. (Nipype default value: 10)

  • out_file (a pathlike object or string representing a file) – Output file. Maps to a command-line argument: -o %s.

  • stop_crit (a float) – Stopping criterion. Maps to a command-line argument: -s %.4f. (Nipype default value: 0.01)

Outputs:

out_file (a pathlike object or string representing a file) – Output file.