From MRI to Functional and Structural Connectivity
Neuroimaging data preprocessing pipeline
Pipeline Video Tutorial
Direct link to notebook
What can I find here?
- an IPython notebook that describes how to
- use the TVB pipeline on one of the associated supercomputers using PyUnicore
- upload model data to the supercomputer
- set up and run the pipeline
- download processing results
How do I use it?
- the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)
- the containers are executed on supercomputers and operated via IPython notebooks
- Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"
- Direct link to notebook: https://drive.ebrains.eu/#my-libs/lib/42ac27a5-981e-4cf6-8ec5-d67b0c24bf09/notebooks
- To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.
- Then, head over to https://lab.ebrains.eu/ to edit and run your notebook.
- Depending on whether you created a public or a private notebook it will be accessible in either "drive/Shared with all" or "drive/Shared with groups'"
Metadata
- Partners: Charité Universitätsmedizin Berlin
- Developers: Michael Schirner (michael.schirner@charite.de), Paul Triebkorn
- Support: Petra Ritter (petra.ritter@charite.de)
- Homepage: https://www.brainsimulation.org
- Documentation: https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view
- Download as Docker image: https://hub.docker.com/r/thevirtualbrain/tvb_converter
- License: GPL3
- Version: 1.0