Getting Started

Installation

Clone the repository:

# Clone the repository
git clone https://github.com/MICA-LAB/micaflow.git
cd micaflow

# Install the package
pip install -e .

Basic Usage

MicaFlow can be used as a complete pipeline or as individual modules:

# Run the full pipeline
micaflow pipeline --subject sub-001 --session ses-01 \
  --data-directory /path/to/data --t1w-file sub-001_ses-01_T1w.nii.gz \
  --out-dir /output --cores 4

Dependencies

MicaFlow requires:

Python 3.9, 3.10, or 3.11