nipype.interfaces.petpvc module

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

PETPVC

Link to code

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

fwhm_xa float

The full-width at half maximum in mm along x-axis. Maps to a command-line argument: -x %.4f.

fwhm_ya float

The full-width at half maximum in mm along y-axis. Maps to a command-line argument: -y %.4f.

fwhm_za float

The full-width at half maximum in mm along z-axis. Maps to a command-line argument: -z %.4f.

in_filea pathlike object or string representing an existing file

PET image file. Maps to a command-line argument: -i %s.

mask_filea 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.

alphaa float

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

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

debuga boolean

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

environa 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_deconvan integer

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

n_iteran integer

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

out_filea pathlike object or string representing a file

Output file. Maps to a command-line argument: -o %s.

stop_crita float

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

out_filea pathlike object or string representing a file

Output file.