CTlessPET for synthetic CT from NAC PET data
Project description
CTlessPET
Install
pip install CTlessPET
Use
CTlessPET only requires an NAC-PET dataset and a CT dataset. The CT is used as the container for the synthetic CT, and can be an empty CT acquired before the patient enters the scanner. The NAC-PET should be reconstructed using OSEM with Time-of-Flight enabled.
Dicom data
Using a folder containing both NAC and CT data:
CTlessPET -i <input_folder> --output <output_folder>
or in seperate folders:
CTlessPET -i <input_NAC_folder> --CT <input_CT_folder> --output <output_folder>
Nifti data
CTlessPET -i <input_NAC_nii> --CT <input_CT_nii> --output <output_nii>
Choice of model
The network has been trained for FDG-PET (adult and pediatric) as well as H20-PET.
The type is automatically selected when running the model with dicom data. You can overwrite the choice of the model using the --model
flag, e.g. --model FDG_Pediatric
.
Optional arguments
You can change the batch size using --batch_size
as well as overwrite the dose (--dose
) and weight (--weight
) given to the patient. This is otherwise automatically read from the dicom file (if supplied).
Citation
If you are using CTlessPET, please cite the following paper:
Montgomery ME, Andersen FL, d’Este SH, Overbeck N, Cramon PK, Law I, Fischer BM, Ladefoged CN. Attenuation Correction of Long Axial Field-of-View Positron Emission Tomography Using Synthetic Computed Tomography Derived from the Emission Data: Application to Low-Count Studies and Multiple Tracers. Diagnostics. 2023; 13(24):3661. https://doi.org/10.3390/diagnostics13243661
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