API Reference

This section provides detailed documentation for all CHIMERA modules, classes, and functions.

CHIMERA Package Overview

CHIMERA: An open source framework for combining multiple parcellations.

Core Classes and Functions

Chimera Class

The main class for creating and working with CHIMERA parcellations.

Main Methods:

Core Functions

Configuration Management

Functions for loading and managing parcellation configurations.

chimera.config_manager.load_parcellations_info(parc_json: str = None, supra_folder: str = None)[source]

Load the JSON file containing the available parcellations

Parameters:

parc_jsonstr: JSON file containing the parcellation dictionary.
supra_folderstr: Folder containing the supraregions TSV files.

Returns:

parc_dictdict: Dictionary containing the parcellation information
supra_dictdict: Dictionary containing the supraregions information

Key Functions:

chimera.config_manager.load_parcellations_info(parc_json: str = None, supra_folder: str = None)[source]

Load the JSON file containing the available parcellations

Parameters:

parc_jsonstr: JSON file containing the parcellation dictionary.
supra_folderstr: Folder containing the supraregions TSV files.

Returns:

parc_dictdict: Dictionary containing the parcellation information
supra_dictdict: Dictionary containing the supraregions information

chimera.config_manager._pipeline_info(pipe_json: str = None)[source]

Load the JSON file containing the pipeline configuration.

Parameters:

pipe_jsonstr: JSON file containing the pipeline configuration dictionary.

Returns:

pipe_dictdict: Dictionary containing the pipeline information

chimera.config_manager._set_templateflow_home(tflow_home: str = 'local')[source]

Setting up the templateflow home directory.

Parameters:

tflow_homestr or Path: Templatefow home directory.

Returns:

updated_tflow_homestr: Updated templateflow home directory.

Parcellation Tools

Tools for creating and manipulating parcellations.

Key Functions:

Processing Tools

External processing tools and utilities.

chimera.processing.launch_fsl_first(t1: str, first_parc: str, cont_tech: str = 'local', cont_image: str = None, force=False)[source]

This function executes the FIRST subcortical parcellation.

Parameters:

t1str: T1-weighted image filename.
first_parcstr: Ouput name for the resulting parcellation.
cont_techstr: Container technology (e.g. singularity, docker or local).
cont_imagestr: Container image.
forcebool: Overwrite the results.

Returns:

Key Functions:

chimera.processing.launch_fsl_first(t1: str, first_parc: str, cont_tech: str = 'local', cont_image: str = None, force=False)[source]

This function executes the FIRST subcortical parcellation.

Parameters:

t1str: T1-weighted image filename.
first_parcstr: Ouput name for the resulting parcellation.
cont_techstr: Container technology (e.g. singularity, docker or local).
cont_imagestr: Container image.
forcebool: Overwrite the results.

Returns:

Data Submodules

Configuration Data

Top-level package for CHIMERA: An open source framework for combining multiple parcellations.

Atlas Data

Top-level package for CHIMERA: An open source framework for combining multiple parcellations.