Getting Started

Install Radiome

Clone the public repository

$ git clone https://github.com/radiome-lab/radiome.git

and install

$ python setup.py install

or

pip install git+https://github.com/radiome-lab/radiome.git

Install Workflow

To build a pipeline in Radiome, you need some workflows.

Install them use pip:

$ pip install workflow-name

Note that some workflows may require specific software packages (e.g. AFNI, ANTs or FSL). You must set up them correctly.

Create Pipeline Config

You need a config file to invoke the workflows with required parameters and combine various workflows into a data pipeline. Please refer to pipeline for more information.

Run

You are all set now! Prepare image resources and put them in a local directory or an S3 bucket you have access to. Make sure the naming is BIDS-compliant.

Run:

$ radiome inputs_location outputs_location --config_file pipeline_config_location

Outputs will be produced in outputs_location/derivatives/{workflow_name}, and organized based on BIDS standard.