conn2combat - Extract First Level Data From CONN For Use With COMBAT.

This script is designed to parse .mat files generated from CONN first-level ROI-to_ROI analyses (https://web.conn-toolbox.org/resources) and output them in a format that can be used by COMBAT (https://github.com/Jfortin1/ComBatHarmonization).

Inputs are the CONN analysis directory, an output directory where the outputs should be stored, (optional) a list of ROIs of interest, and (optional) whether outputs should be limited to ROI-to-ROI.

Outputs consist of one CSV file per subject containing the correlation data for each ROI, and a combined CSV file containing all subjects' data.

Options

• -d, --conn_directory: Path to the CONN analysis directory. Required.
• -o, --output_directory: Path to the directory where the outputs will be saved. Default is the current directory.
• -r, --rois: List of regions of interest (ROIs) to export. Default is all ROIs.
• -l, --limit: Limits output to only ROI-to-ROI data (as opposed to ROIs-to-all including atlas and networks).

Example

combat2conn -d /path/to/conn_directory -o /path/to/output_dir -r ROI1 ROI2 ROI3

Requirements

• Python 3.x (tested with python 3.11.11)

Install as package

1. Install using pip:

   pip install conn2combat
   

2. Process files:

   python -m combat2conn -d /path/to/conn_directory -o /path/to/output_dir -r ROI1 ROI2 ROI3
   

Run from source

1. Clone the repository:

   git clone https://github.com/trevorbryanjackson/CONN_First_Level_Extraction.git
   

2. Navigate to the project directory:

   cd CONN_First_Level_Extraction
   

3. Install the required dependencies:

   pip install -r requirements.txt
   

4. Process CONN directory:

   python conn2combat.py -d /path/to/conn_directory -o /path/to/output_dir -r ROI1 ROI2 ROI3