Installation

Stable release (pip)

To install fMRI from PyPI with pip:

$ pip install fmri

This installs the latest stable release and the CLI entry points (fmri-main, preprocess-nii-file, nifti-viewer, compare-pcs).

Windows (recommended: conda/mamba)

On Windows we recommend using a conda environment (via Miniconda or Mambaforge) for smooth installation of scientific dependencies:

1. Install Miniconda or Mambaforge

   • Miniconda: https://docs.conda.io/en/latest/miniconda.html

   • Mambaforge: https://github.com/conda-forge/miniforge

2. Create and activate an environment (Python 3.11 suggested)

# Install mamba in base (optional but faster)
conda install -c conda-forge mamba

# Create environment
mamba create -n fmri-env -c conda-forge python=3.11

# Activate environment
mamba activate fmri-env

3. Install core scientific packages from conda-forge (ensures MKL/OpenBLAS are configured correctly)

mamba install -c conda-forge numpy scipy mkl mkl-service matplotlib nibabel scikit-fda dtaidistance

4. Install the fMRI package (PyPI) into the same environment

pip install fmri

From sources

The sources for fMRI can be downloaded from the Github repo.

Clone the repository:

$ git clone https://github.com/yanivassf-lab/fmri
$ cd fmri

Install in editable mode (development):

# Option A: system Python
$ pip install -e .

# Option B: conda
$ conda install -c conda-forge mamba
$ mamba create -n fmri-dev -c conda-forge python=3.11
$ mamba activate fmri-dev
$ mamba install -c conda-forge numpy scipy mkl mkl-service matplotlib nibabel scikit-fda dtaidistance
$ pip install -e .

Verify installation

fmri-main --help
preprocess-nii-file --help
compare-pcs --help