CONN Tool Manager

A lightweight, cross-platform GUI designed for fMRI researchers using the CONN toolbox and fMRIPrep. This tool simplifies data reorganization, participant ID mapping, and lightweight project exporting for second-level analysis.

🚀 Key Features

• Reorganize Data: Standardizes fMRIPrep output across single and multi-session subjects to ensure CONN compatibility.
• Map CONN IDs: Automatically maps BIDS sub-<label> IDs to CONN's internal subject 1, 2, 3... IDs by parsing project logs.
• Lightweight Export: Creates a "portable" version of your CONN project by excluding heavy denoised functional volumes (DATA_*.mat), allowing you to perform second-level statistics on a laptop without moving hundreds of GBs.
• Cross-Platform GUI: Built with Flask and Waitress, running in your web browser with a built-in terminal for status tracking.
• Standalone Build: Can be compiled into a single executable for Windows, macOS, and Linux.

🛠 Installation (Developer Mode)

1. Install dependencies: Make sure you have uv installed for the fastest setup.

   python install_gui.py

2. Run the application:

   # macOS/Linux
   ./.venv/bin/python app.py
   
   # Windows
   .venv\Scripts\python.exe app.py

📦 Standalone Downloads

If you are using a version downloaded from the GitHub Releases page, simply extract the file and run it. No Python installation is required.

📋 Usage Guide

1. Reorganize Data

Point the tool to your BIDS root directory. It will ensure that anatomical files are correctly placed and JSON/HTML references are updated so CONN can find your data consistently.

2. Map IDs

Select your conn_project.mat and your BIDS folder. The tool will generate a participants_with_conn.tsv file containing the mapping between your BIDS IDs and CONN subject indices.

3. Lightweight Export

Perfect for moving projects.

• Source: Your main .mat file.
• Destination: A new folder (e.g., on a portable drive).
• Result: A project containing only first-level results and ROI data, optimized for group statistics.

🔬 Lab Information

Developed for the MRI Lab Graz.

• GitHub: https://github.com/MRI-Lab-Graz/
• Maintainer: Karl (MRI Lab Graz)

---

Disclaimer: This tool is not an official part of the CONN toolbox. Always back up your data before performing batch reorganization.