Outputs

PETFit produces output files following BIDS derivatives conventions. All outputs go into the derivatives/petfit/ directory.

Directory structure

bids_directory/                           # Raw BIDS data
├── participants.tsv
├── code/petfit/
│   └── petfit_regions.tsv                # Region definitions
└── sub-*/ses-*/pet/

derivatives/                              # Processed outputs
└── petfit/                               # PETFit outputs
    ├── petfit_regions.tsv                # Region definitions (copy)
    ├── desc-combinedregions_tacs.tsv     # Combined TACs (all regions)
    └── Analysis_Name/                    # Analysis-specific folder
        ├── desc-petfitoptions_config.json
        ├── sub-01/
        │   ├── sub-01_desc-combinedregions_tacs.tsv
        │   ├── sub-01_desc-weights_weights.tsv
        │   └── sub-01_model-2TCM_kinpar.tsv
        ├── sub-02/
        │   └── ...
        └── reports/
            ├── data_definition_report.html
            ├── weights_report.html
            ├── delay_report.html
            ├── model1_report.html
            └── ...

Region definition outputs

These files are shared across all analyses.

petfit_regions.tsv

The region definition file listing all combined regions and their constituents. This file can be transferred between studies that use the same preprocessing pipelines and segmentations.

desc-combinedregions_tacs.tsv

The combined TACs file containing all PET measurements and regions with BIDS metadata.

Modelling outputs

These files are created within analysis-specific subfolders.

Individual TAC files

One file per PET measurement, named {pet_id}_desc-combinedregions_tacs.tsv.

Weight files

One file per PET measurement, named {pet_id}_desc-weights_weights.tsv. Contains per-frame weights for each region.

Kinetic parameter files

One file per PET measurement per model, named {pet_id}_model-{MODEL}_kinpar.tsv. Contains the fitted kinetic parameters for each region._ There is also a global kinetic parameter file for all subjects in the analysis created in the main analysis folder, named model_{MODEL}_desc-{MODEL_NUMBER}_kinpar.tsv

Configuration file

desc-petfitoptions_config.json stores all analysis settings. This file is generated automatically by the interactive apps and read by the automatic pipeline.

HTML reports

Generated in the reports/ subdirectory. See Parameterised reports for details.

BIDS metadata integration

PETFit automatically integrates data from your BIDS dataset into the combined TACs:

Participant data — Reads participants.tsv and participants.json from the BIDS root. Maps participant_id format (sub-01 to 01) and extracts body weight for SUV calculations.
PET metadata — Extracts InjectedRadioactivity from PET JSON sidecars and converts units to kBq.