This is a repo of software configuration and Jupyter notebooks for the TVB app on the HIP platform, as part of HBP SGA3. It is a work in progress, but the following diagram shows the functional structure:
The app consists of a tvb_hip Python module and template Jupyter notebooks.
The Python code assumes that a variety of tools are already installed:
- Freesurfer
- FSL
- Mrtrix3
- Python + JupyterLab and all dependencies
Data is processed inside temporary FreeSurfer $SUBJECTS_DIR/$SUBJECT folders.
For local development, I install the above tools, use a virtualenv for the Python environment, and use Jupyter via a normal browser.
This environment requires synchronizing some data via nextcloud client somewhere
on disk, and then the tvb_hip module should pick up via env var hip_nextcloud.
For HIP, a Docker image contains the above tools + JupyterLab Desktop,
with data is present under ~/nextcloud, available directly on the HIP platform:
