BIDSKIT Installation

March 27, 2019 ยท View on GitHub

BIDSKIT can be installed from GitHub source or from PyPI using the pip command

Requirements

bidskit was developed for Python 3.7 and depends on several popular packages including numpy and pydicom. Python dependencies are handled through setuptools (setup.py) during installation.

dcm2niix

bidskit also requires that dcm2nixx version 1.0.20181125 or later. See Chris Rorden's GitHub repository for detailed installation instructions.

GitHub Installation

  1. Clone this branch to your local system 
    % git clone https://github.com/jmtyszka/bidskit.git
  2. Install to your local Python 3 environment 
    % cd bidskit
% [sudo] python3 setup.py install

PyPI Installation

  1. Install the latest Python 3 version of bidskit from PyPI 
    % [sudo] pip3 install bidskit

Optional Extensions

bids-validator

We recommend installing the Node.js application bids-validator for post-conversion validation from within bidskit.

  1. Install Node.js (version 8.0 or later)
  2. Install bids-validator 
    % npm install -g bids-validator