Getting Started

Installation

You can install MicaFlow directly via pip:

pip install micaflow
# Verify installation
micaflow

Or, install from source:

# Clone the repository
git clone https://github.com/MICA-MNI/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 for a single subject
micaflow pipeline --subject sub-001 --session ses-01 \
  --data-directory /path/to/data --t1w-file sub-001_ses-01_T1w.nii.gz \
  --output /output --cores 4

Batch Processing (BIDS)

To process an entire BIDS dataset automatically, you can use the batch command. This will scan the BIDS directory for valid subjects/sessions, identify required files based on suffixes, run the pipeline sequentially, and generate a micaflow_runs_summary.json file:

micaflow bids --bids-dir /path/to/bids_root --output-dir /path/to/derivatives \
  --cores 4 --gpu

You can restrict processing to specific subsets using --participant-label (e.g., 001 002) and --session-label.

Dependencies

MicaFlow requires:

Python 3.9, 3.10, or 3.11