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improve petpvc documentation
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‎nipype/interfaces/petpvc.py

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>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
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>>> os.chdir(datadir)
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Nipype interface for PETPVC.
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PETPVC is a software from the Nuclear Medicine Department
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of the UCL University Hospital, London, UK.
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Its source code is here: https://github.com/UCL/PETPVC
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The methods that it implement are explained here:
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K. Erlandsson, I. Buvat, P. H. Pretorius, B. A. Thomas, and B. F. Hutton,
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"A review of partial volume correction techniques for emission tomography
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and their applications in neurology, cardiology and oncology," Phys. Med.
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Biol., vol. 57, no. 21, p. R119, 2012.
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There is a publication waiting to be accepted for this software tool.
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Its command line help shows this:
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-i --input < filename >
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= PET image file
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-o --output < filename >
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= Output file
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[ -m --mask < filename > ]
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= Mask image file
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-p --pvc < keyword >
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= Desired PVC method
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-x < X >
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= The full-width at half maximum in mm along x-axis
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-y < Y >
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= The full-width at half maximum in mm along y-axis
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-z < Z >
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= The full-width at half maximum in mm along z-axis
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[ -d --debug ]
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= Prints debug information
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[ -n --iter [ Val ] ]
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= Number of iterations
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With: Val (Default = 10)
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[ -k [ Val ] ]
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= Number of deconvolution iterations
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With: Val (Default = 10)
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[ -a --alpha [ aval ] ]
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= Alpha value
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With: aval (Default = 1.5)
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[ -s --stop [ stopval ] ]
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= Stopping criterion
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With: stopval (Default = 0.01)
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----------------------------------------------
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Technique - keyword
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Geometric transfer matrix - "GTM"
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Labbe approach - "LABBE"
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Richardson-Lucy - "RL"
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Van-Cittert - "VC"
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Region-based voxel-wise correction - "RBV"
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RBV with Labbe - "LABBE+RBV"
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RBV with Van-Cittert - "RBV+VC"
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RBV with Richardson-Lucy - "RBV+RL"
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RBV with Labbe and Van-Cittert - "LABBE+RBV+VC"
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RBV with Labbe and Richardson-Lucy- "LABBE+RBV+RL"
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Multi-target correction - "MTC"
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MTC with Labbe - "LABBE+MTC"
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MTC with Van-Cittert - "MTC+VC"
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MTC with Richardson-Lucy - "MTC+RL"
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MTC with Labbe and Van-Cittert - "LABBE+MTC+VC"
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MTC with Labbe and Richardson-Lucy- "LABBE+MTC+RL"
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Iterative Yang - "IY"
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Iterative Yang with Van-Cittert - "IY+VC"
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Iterative Yang with Richardson-Lucy - "IY+RL"
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Muller Gartner - "MG"
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Muller Gartner with Van-Cittert - "MG+VC"
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Muller Gartner with Richardson-Lucy - "MG+RL"
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"""
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from __future__ import print_function
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from __future__ import division
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@@ -144,6 +71,76 @@ class PETPVCOutputSpec(TraitedSpec):
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class PETPVC(CommandLine):
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""" Use PETPVC for partial volume correction of PET images.
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PETPVC is a software from the Nuclear Medicine Department
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of the UCL University Hospital, London, UK.
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Its source code is here: https://github.com/UCL/PETPVC
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The methods that it implement are explained here:
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K. Erlandsson, I. Buvat, P. H. Pretorius, B. A. Thomas, and B. F. Hutton,
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"A review of partial volume correction techniques for emission tomography
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and their applications in neurology, cardiology and oncology," Phys. Med.
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Biol., vol. 57, no. 21, p. R119, 2012.
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There is a publication waiting to be accepted for this software tool.
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Its command line help shows this:
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-i --input < filename >
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= PET image file
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-o --output < filename >
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= Output file
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[ -m --mask < filename > ]
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= Mask image file
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-p --pvc < keyword >
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= Desired PVC method
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-x < X >
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= The full-width at half maximum in mm along x-axis
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-y < Y >
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= The full-width at half maximum in mm along y-axis
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-z < Z >
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= The full-width at half maximum in mm along z-axis
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[ -d --debug ]
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= Prints debug information
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[ -n --iter [ Val ] ]
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= Number of iterations
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With: Val (Default = 10)
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[ -k [ Val ] ]
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= Number of deconvolution iterations
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With: Val (Default = 10)
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[ -a --alpha [ aval ] ]
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= Alpha value
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With: aval (Default = 1.5)
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[ -s --stop [ stopval ] ]
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= Stopping criterion
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With: stopval (Default = 0.01)
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----------------------------------------------
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Technique - keyword
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Geometric transfer matrix - "GTM"
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Labbe approach - "LABBE"
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Richardson-Lucy - "RL"
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Van-Cittert - "VC"
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Region-based voxel-wise correction - "RBV"
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RBV with Labbe - "LABBE+RBV"
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RBV with Van-Cittert - "RBV+VC"
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RBV with Richardson-Lucy - "RBV+RL"
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RBV with Labbe and Van-Cittert - "LABBE+RBV+VC"
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RBV with Labbe and Richardson-Lucy- "LABBE+RBV+RL"
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Multi-target correction - "MTC"
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MTC with Labbe - "LABBE+MTC"
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MTC with Van-Cittert - "MTC+VC"
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MTC with Richardson-Lucy - "MTC+RL"
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MTC with Labbe and Van-Cittert - "LABBE+MTC+VC"
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MTC with Labbe and Richardson-Lucy- "LABBE+MTC+RL"
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Iterative Yang - "IY"
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Iterative Yang with Van-Cittert - "IY+VC"
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Iterative Yang with Richardson-Lucy - "IY+RL"
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Muller Gartner - "MG"
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Muller Gartner with Van-Cittert - "MG+VC"
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Muller Gartner with Richardson-Lucy - "MG+RL"
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Examples
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--------
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>>> from ..testing import example_data

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