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PETPipelineMATLAB

Description

The PETPipeline pipeline is a state-of-the-art PET preprocessing pipeline (wrapper) for MATLAB. This pipeline is designed to execute multiple preprocessing steps on BIDS structured datasets that have at least one dynamic PET scan and one anatomical MRI scan. The key steps integrated within the pipeline include:

  • Motion correction
  • Co-registration
  • Segmentation
  • Partial volume correction
  • Kinetic modeling

Usage

To utilize the PETPipeline function in your MATLAB environment:

PETPrep(data_dir, config)

Parameters:

  • data_dir (str): This is the path directing to the BIDS data directory.
  • config (str): This is the path directing to the PETPrep configuration file. This config should be placed in a 'code' directory in the main BIDS directory. Example: 'config1.json'.

Note: The function doesn't return any values.

Sequential Steps Enforced by the Pipeline:

  1. Transition to the BIDS data directory.
  2. Integrate BIDS data into MATLAB.
  3. Incorporate the configuration file.
  4. Initiate derivatives directories.
  5. Activate ReconAll for FreeSurfer reconstruction.
  6. Perform GTM segmentation with GTMSeg.
  7. Convert FreeSurfer output to BIDS structure with ConvertFS2BIDS.
  8. Perform motion correction (various methods available).
  9. Co-register with CoReg and plot results with PlotCoReg.
  10. Perform GTM PVC with GTMPVC.
  11. Convert PETsurfer output to BIDS structure with PETsurfer2TAC.
  12. Perform kinetic modeling (various models available).

Author

Martin Norgaard, Stanford University, 2022.

License

[License details, if any]

Acknowledgements

[Optional section for any acknowledgements or citations]