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() #doctest: +SKIP

References

[1]K. Erlandsson, I. Buvat, P. H. Pretorius, B. A. Thomas, and B. F. Hutton, “A review of partial volume correction techniques for emission tomography and their applications in neurology, cardiology and oncology,” Phys. Med. Biol., vol. 57, no. 21, p. R119, 2012.
[2]https://github.com/UCL/PETPVC
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’

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

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

alpha : a float
Alpha value. Maps to a command-line argument: -a %.4f. (Nipype default value: 1.5)
args : a unicode 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 (int or long)
Number of deconvolution iterations. Maps to a command-line argument: -k %d. (Nipype default value: 10)
n_iter : an integer (int or long)
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)
out_file : a pathlike object or string representing a file
Output file.
PETPVC.references_ = [{'entry': None, 'description': 'PETPVC software implementation publication', 'tags': ['implementation']}]