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Installation

Prerequisites

Prerequisites

🔀 Install Nextflow

Follow the Nextflow installation guide.

🐳 Pull Docker image for the BIDS Validator (optional)

Download a Nextflow-compatible BIDS Validator image tailored to your system architecture:

  • Standard Unix systems (amd64)
docker pull agahkarakuzu/bids-validator-amd64
  • Apple silicon (arm64)
docker pull agahkarakuzu/bids-validator-arm64
🍎 Important warning for macOS users

The default bash version on macOS does not meet libBIDS requirements. Install a newer bash with Homebrew:

brew install bash

Then set process.shell in your nextflow.config to:

  • Apple Silicon: /opt/homebrew/bin/bash
  • Intel Macs: /usr/local/bin/bash

🧠 Get bids2nf

After installing the prerequisites, simply clone this repository with its submodules:

git clone --recurse-submodules https://github.com/agahkarakuzu/bids2nf.git

Submodules included

libBIDS.sh

A Bash library for parsing and processing BIDS datasets into CSV-like structures, enabling flexible data filtering, extraction, and iteration within shell scripts.

BIDS examples

A set of BIDS compatible datasets with empty raw data files that can be used for writing lightweight software tests.

What’s Next?

bids2nf
bids2nf
bids2nf
Quick Start