Quick Start Guide

If Python is available, CBPtools and its dependencies can quickly be installed using pip, which is packaged together with Python.

pip install cbptools

After installation, CBPtools can be called directly from the command line using the cbptools command. An example configuration file can be obtained using the example directive:

cbptools example --get modality

The modality argument should be replaced by the type of data you intend to give as input. Currently supported are rsfmri (rsfMRI), dmri (dMRI), and connectivity. A configuration file with default and placeholder settings will be created in the current working directory. Edit this file such that it correctly points to the input data and has the desired configuration values.

With the configuration file and input data in order, an rCBP project can now be set up.

cbptools create --config /path/to/config_file.yaml --workdir /path/to/workdir

Point the –config parameter to the configuration file and the –workdir to the directory in which the project files will be placed. CBPtools will validate the configuration file and input data. If everything is properly formatted, the project will be created in the designated working directory.

Note

It is strongly suggested to read the log file, especially if there are any warnings or errors during the setup.

The next step is to go to the workdir and execute the workflow using snakemake, which is installed as a dependency of CBPtools. Once this is done, the rCBP procedure will start.

cd /path/to/workdir
snakemake

Snakemake has a range of parameters it can be executed with. Common uses with CBPtools are outlined in the Execution section. For more customizability on snakemake, visit the snakemake documentation.