Installing FEDI

There are multiple ways to install the FEDI toolbox.

Installation Methods

Option 1: Install via pip

The easiest way to install FEDI is through pip. Open a terminal and run:

pip install fedi

Option 2: Clone the Repository

To manually install the FEDI toolbox and primarily access its workflows, clone the repository and add the necessary paths to your .bashrc file:

git clone https://github.com/FEDIToolbox/FEDI.git
cd FEDI/FEDI/scripts
FEDI_SCRIPTS=$(pwd)
echo 'export PATH="${FEDI_SCRIPTS}:$PATH"' >> ~/.bashrc
source ~/.bashrc

Workflows such as HAITCH are available in:

cd FEDI/FEDI/pipelines

Option 3: Conda Environment (Coming Soon)

We are currently working on providing an installation option via Conda for easier dependency management.

Verifying Installation

After installing FEDI, we recommend verifying that the installation is working correctly by running the automated test suite:

fedi_testing

This command will:

Generate synthetic test data: Creates realistic 4D diffusion MRI data with fixed parameters in ~/.fedi_test_data/
Run automated tests: Tests all FEDI command-line tools and verifies that they execute correctly and produce expected outputs

The test suite will report which tools passed, failed, or were skipped (due to missing optional dependencies). Some tests may take several minutes to complete, especially fedi_dmri_moco and fedi_dmri_recon.

For more information about the testing command, see fedi_testing.

Dependencies

FEDI supports DICOM, NIfTI, and MIF image formats and relies on several external dependencies for full functionality. We strongly recommend using the Anaconda Python distribution to manage dependencies efficiently.

Required Python Packages:

These packages are automatically installed when you install FEDI via pip:

NumPy - Numerical computing
SciPy - Scientific computing
NiBabel - Neuroimaging file I/O
Matplotlib - Plotting and visualization
DIPY - Diffusion imaging in Python
CVXPY - Convex optimization
Healpy - Spherical harmonics and HEALPix

Required for Specific Features:

PyTorch - Required for fedi_dmri_fod (FOD estimation)
Hugging Face Hub - Required for fedi_dmri_fod (model downloads)

Required External Tools:

MRtrix3
ANTs

Getting Help

For questions, issues, or suggestions, please open an issue on our GitHub repository.