nipype.interfaces.petpvc module¶
PETPVC is a toolbox for partial volume correction in positron emission tomography.
PETPVC¶
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.