Cli Reference Tissue Models#

This module provides a command-line interface for running various reference tissue model (RTM) analyses.

The module defines a set of command-line arguments for the input and output data, as well as the analysis specifics. Several types of RTM analyses, such as SRTM, FRTM, MRTM and its variants, are supported, each with its associated arguments.

The primary function in the module is main(), which is responsible for parsing command-line arguments, running the selected analysis, and handling the results. The analysis is performed using the RTMAnalysis class.

Example

Assuming that the package has been installed, we have:

For running an FRTM analysis:

petpal-rtms frtm --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --initial-guesses 0.1 0.1 0.1 0.1 0.1 --lower-bounds 0.0 0.0 0.0 0.0 0.0 --upper-bounds 5.0 5.0 5.0 5.0 5.0

For running an SRTM analysis:

petpal-rtms srtm --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --initial-guesses 0.1 0.1 0.1 0.1 0.1 --lower-bounds 0.0 0.0 0.0 0.0 0.0 --upper-bounds 5.0 5.0 5.0 5.0 5.0

For running an FRTM2 analysis:

petpal-rtms frtm2 --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --k2-prime 0.5 --prefix sub_001 --print --initial-guesses 0.1 0.1 0.1 --lower-bounds 0.0 0.0 0.0 --upper-bounds 5.0 5.0 5.0

For running an SRTM2 analysis:

petpal-rtms srtm2 --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --k2-prime 0.5 --prefix sub_001 --print --initial-guesses 0.1 0.1 --lower-bounds 0.0 0.0 0.0 --upper-bounds 5.0 5.0

For running an MRTM analysis:

petpal-rtms mrtm --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --t-thresh-in-mins 30.0

For running an MRTM2 analysis:

petpal-rtms mrtm2 --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --t-thresh-in-mins 30.0 --k2-prime 0.1

For running the original MRTM analysis:

petpal-rtms mrtm-original --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --t-thresh-in-mins 30.0

See also

  • petpal.reference_tissue_models

Attributes#

_RTM_EXAMPLES_

Functions#

add_common_args(parser)

Adds common arguments to an ArgumentParser object.

parse_args()

Defines and parses command-line arguments.

_generate_bounds(→ Union[numpy.ndarray, None])

Generates the bounds for the fitting parameters.

_pretty_print_results(→ None)

Formats and prints the analysis results to the console.

Module Contents#

petpal.cli.cli_reference_tissue_models._RTM_EXAMPLES_ = Multiline-String#
Show Value
"""
Examples:
  - FRTM (4 parameters: R1, k2, k3, k4):
    petpal-rtms frtm --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --initial-guesses 0.1 0.1 0.1 0.1 --lower-bounds 0.0 0.0 0.0 0.0 --upper-bounds 5.0 5.0 5.0 5.0
  - SRTM (3 parameters: R1, k2, BP):
    petpal-rtms srtm --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --initial-guesses 0.1 0.1 0.1 --lower-bounds 0.0 0.0 0.0 --upper-bounds 5.0 5.0 5.0
  - FRTM2 (3 parameters: R1, k3, k4):
    petpal-rtms frtm2 --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --k2-prime 0.5 --prefix sub_001 --print --initial-guesses 0.1 0.1 0.1 0.1 --lower-bounds 0.0 0.0 0.0 0.0 --upper-bounds 5.0 5.0 5.0 5.0
  - SRTM2 (2 parameters: R1, BP):
    petpal-rtms srtm2 --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --k2-prime 0.5 --prefix sub_001 --print --initial-guesses 0.1 0.1 0.1 0.1 --lower-bounds 0.0 0.0 0.0 --upper-bounds 5.0 5.0
  - MRTM (2 parameters: BP, k2_prime):
    petpal-rtms mrtm --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --t-thresh-in-mins 30.0
  - MRTM2 (2 parameters: BP):
    petpal-rtms mrtm2 --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --t-thresh-in-mins 30.0 --k2-prime 0.1
  - MRTM (Original) (2 parameters: BP, k2_prime):
    petpal-rtms mrtm-original --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --t-thresh-in-mins 30.0
"""