interfaces.petpvc¶
PETPVC¶
Wraps the executable command petpvc
.
Use PETPVC for partial volume correction of PET images.
PETPVC is a software from the Nuclear Medicine Department of the UCL University Hospital, London, UK.
Its source code is here: https://github.com/UCL/PETPVC
The methods that it implement are explained here: 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.
Its command line help shows this:
- -i –input < filename >
- = PET image file
- -o –output < filename >
- = Output file
- [ -m –mask < filename > ]
- = Mask image file
- -p –pvc < keyword >
- = Desired PVC method
-x < X > = The full-width at half maximum in mm along x-axis -y < Y > = The full-width at half maximum in mm along y-axis -z < Z > = The full-width at half maximum in mm along z-axis
- [ -d –debug ]
- = Prints debug information
- [ -n –iter [ Val ] ]
- = Number of iterations
- With: Val (Default = 10)
- [ -k [ Val ] ]
- = Number of deconvolution iterations
- With: Val (Default = 10)
- [ -a –alpha [ aval ] ]
- = Alpha value
- With: aval (Default = 1.5)
- [ -s –stop [ stopval ] ]
- = Stopping criterion
- With: stopval (Default = 0.01)
Technique - keyword¶
- 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”
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()
Inputs:
[Mandatory]
in_file: (an existing file name)
PET image file
argument: ``-i %s``
mask_file: (an existing file name)
Mask image file
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
argument: ``-p %s``
fwhm_x: (a float)
The full-width at half maximum in mm along x-axis
argument: ``-x %.4f``
fwhm_y: (a float)
The full-width at half maximum in mm along y-axis
argument: ``-y %.4f``
fwhm_z: (a float)
The full-width at half maximum in mm along z-axis
argument: ``-z %.4f``
[Optional]
out_file: (a file name)
Output file
argument: ``-o %s``
debug: (a boolean, nipype default value: False)
Prints debug information
argument: ``-d``
n_iter: (an integer (int or long), nipype default value: 10)
Number of iterations
argument: ``-n %d``
n_deconv: (an integer (int or long), nipype default value: 10)
Number of deconvolution iterations
argument: ``-k %d``
alpha: (a float, nipype default value: 1.5)
Alpha value
argument: ``-a %.4f``
stop_crit: (a float, nipype default value: 0.01)
Stopping criterion
argument: ``-a %.4f``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
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
Outputs:
out_file: (a file name)
Output file
References:¶
None