fw-heudiconv can be run in the Flywheel GUI as a gear, or locally using the
Command Line Interface distributed using pip.
flaudit can only be run
in the Flywheel GUI.
FlywheelTools are intended for use with a Flywheel site. At the University of Pennsylvania, our site is available at upenn.flywheel.io.
To use locally, follow instructions below to set up your system for using
fw-heudiconv on your machine:
Estimated time: 15 minutes
Install & start up Miniconda¶
First, get a package management system. Recommended is miniconda (conda): Conda quickly installs, runs and updates packages and their dependencies.
You can check if you have this successfully by going to the terminal and doing:
$ which conda [macOS]
Start a virtual environment¶
Use miniconda to create a virtual environment, a restricted workspace where your programs and processes can operate without affecting everything on your computer. Create an environment called flywheel, in the terminal:
$ conda create -n flywheel anaconda python=3
At the prompt for which packages to install, type y and hit enter. It’s better to have them all, and they will not take up a lot of space on your machine:
: : : $ wurlitzer pkgs/main/osx-64::wurlitzer-1.0.2-py37_0 $ xlrd pkgs/main/osx-64::xlrd-1.2.0-py37_0 $ xlsxwriter pkgs/main/noarch::xlsxwriter-1.1.8-py_0 $ xlwings pkgs/main/osx-64::xlwings-0.15.8-py37_0 $ xlwt pkgs/main/osx-64::xlwt-1.3.0-py37_0 $ xz pkgs/main/osx-64::xz-5.2.4-h1de35cc_4 $ yaml pkgs/main/osx-64::yaml-0.1.7-hc338f04_2 $ zeromq pkgs/main/osx-64::zeromq-4.3.1-h0a44026_3 $ zict pkgs/main/noarch::zict-1.0.0-py_0 $ zipp pkgs/main/noarch::zipp-0.5.1-py_0 $ zlib pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3 $ zstd pkgs/main/osx-64::zstd-1.3.7-h5bba6e5_0 $ Proceed ([y]/n)?
Activate your environment, so that any packages you install or use stay restricted to this project:
$ source activate flywheel
fw-heudiconv from pip¶
fw-heudiconv code is hosted on pip: pip is a standard package-management system used to install and manage software packages written in Python
Pip should be installed with your new environment, but you can ensure you have it by running:
$ which pip
Now, use pip to install
$ pip install fw-heudiconv
Download the Flywheel SDK & CLI¶
You will need to download the flywheel software development kit in order to use
fw-heudiconv. Follow the instructions here to install, or run:
$ pip install flywheel-sdk
The flywheel CLI allows
fw-heudiconv (or any other program you write) to communicate with Flywheel’s database. Follow their instructions here to download and login.
Once installed and logged in, you should see your username when you run the following:
$ fw status $ You are currently logged in as Tinashe Tapera to https://upenn.flywheel.io
If you already have
fw-heudiconv and wish to update to the latest version, just run:
$ pip install --upgrade fw-heudiconv
fw-heudiconv-validate is a convenience tool that wraps the official Bids Validator and pipes the output of
fw-heudiconv-export to it. It’s most useful for validating Flywheel data through a gear on the GUI.
fw-heuduiconv-validate on your local machine, you need to install node.js. This is not necessary, however, and instead you are welcome to use
fw-heudiconv-validate on your Flywheel site, or, use
fw-heudiconv-export to export data first, and then use the official Bids Validator available here.