Affects Version/s: None
Fix Version/s: None
This story describes one of the projects proposed for the GSOC 2020. The student working on this is Punit Batra. We will add subtasks to this story, during the GSOC 2020 timeline based on discussions with the student.
A real brain can turn to a virtual brain in 3 steps. First, the patient goes to a RMN scanner, then, the measured images go through a reconstruction pipeline, and finally, the results are uploaded in TVB. This reconstruction pipeline is a mandatory tool, it takes RMN images, processes them and extracts the brain’s connectivity, geometry, parcellations and other data necessary for virtualization. It produces files that are compatible with TVB. Links together tools like Freesurfer, MRtrix, FSL, Pegasus WMS.
We host a lightweight version of such a reconstruction pipeline here: https://github.com/the-virtual-brain/tvb-recon 9
Providing a GUI for such a pipeline would greatly improve our user experience. This interface should allow users to provide input data, choose configurations, define the output structure, launch the workflow and monitor progress. Additionally it would be nice to integrate with our workflow engine (Pegasus) in order to provide job status and job execution statistics.
The GUI design is open to suggestions. Share your creativity with us!
Expected results: Web based GUI for tvb-recon
Skills: Python, HTML5, CSS, JS, experience in web development