Installation

NiSpace is not yet available on PyPI and has to be installed from GitHub.

Requirements

NiSpace requires Python 3.9+. We recommend installation in a dedicated environment (e.g., via Mamba). The implemented imaging space transformations rely on neuromaps, which in turn uses Connectome Workbench to transform data from volume to surface spaces or resample surface files. If you use this functionality, make sure that you have Workbench installed (see neuromaps installation instructions).

Installation via pip from GitHub

The current development version is most conveniently installed from GitHub using pip:

pip install git+https://github.com/LeonDLotter/NiSpace.git@dev

For reproducibility, consider installing a specific commit:

pip install git+https://github.com/LeonDLotter/NiSpace.git@{commit_hash}

There are currently two optional dependencies: factor-analyzer and BrainSmash. When calling the respective NiSpace functions, you are prompted to install them. However, to avoid this, you can install them directly with the other dependencies using:

pip install "git+https://github.com/LeonDLotter/NiSpace.git@dev#egg=nispace[opt]"

In the future, factor-analyzer will be removed as a dependency and all non-default null models will be kept as optional dependencies. The default null model, moran, was copied from BrainSpace and integrated into NiSpace to avoid BrainSpace and vtk as dependencies.

Installation from source

Alternatively, you can clone the repository and install NiSpace manually:

git clone https://github.com/LeonDLotter/NiSpace.git
cd NiSpace
pip install .

Installation via pip from PyPI

NiSpace is not yet available on PyPI.

Integrated data

Data (parcellations, templates, reference maps, …) are downloaded automatically when you run fetch_... functions.