FreeSurfer to BIDS Converter

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🧠 Overview

This module provides a lightweight Python utility to convert FreeSurfer output directories into a **BIDS-compatible structure **.
It reorganizes nested FreeSurfer data, verifies integrity through size checks, and supports both dry-run and move/copy modes.

This tool helps researchers working with FreeSurfer outputs standardize their data within a consistent BIDS derivatives hierarchy such as:

derivatives/
├── freesurfer_v7.1.1/
│    ├── sub-00001/
│    │      ├── ses-001/
│    │      │    ├── channels.txt
│    │      │    ├── label/
│    │      │    ├── mri/
│    │      │    ├── scripts/
│    │      │    ├── stats/
│    │      │    ├── surf/
│    │      │    ├── tmp/
│    │      │    ├── touch/
│    │      │    ├── trash/
│    │      │    ├── xhemi/
│    │      │    └── xhemi-textures.npy
│    │      ├── ses-002/
│    │      └── ses-003/
│    ├── sub-00002/
│    └── sub-00003/

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⚙️ Installation

Requirements

• Python 3.8+
• Standard library modules only:
  • logging
  • pathlib
  • shutil

No external dependencies are required.

Clone this repository

git clone https://github.com/nasirone/FreeSurferToBIDS.git
cd FreeSurferToBIDS