Roy G. Brain Image Viewer for browser-based visualization of Mindboggle cortical surface label/shape data
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roygbiv
.gitignore
README.md
get_data.py
license.txt
requirements.txt
server.py

README.md

roygbiv (Roy G. Brain Image Viewer) is an interactive browser-based visualization of cortical surfaces.

Instructions for running demos are below. To run demos locally, install the flask Python package.

###To set up the main demo locally:

  1. Run python get_data.py demo. This will download sample data files.
  2. Run server.py to launch a light-weight web server
  3. Browse to http://127.0.0.1:5000/

###To set up the two hemis demo locally:

  1. Install vtk
  2. Install mindboggle (pip install git+https://github.com/binarybottle/mindboggle.git)
  3. Run python get_data.py fsaverage (or replace `fsaverage with your desired freesurfer subject)
  4. Run python server.py to launch a light-weight web server
  5. Browse to http://127.0.0.1:5000/fsaverage/desikan/pial/two_hemis.html

You can change parameters above and change the corresponding URL: * Use your subject ID instead of fsaverage, if you have your own data. * Use --atlas destrieux to use a smaller parcellation. * Use --surface inflated to view an inflated surface.

###To deploy your files remotely

  1. Create the data (see above)
  2. Upload all files to your remote web server (html, json, css, data)
  3. Browse to http://your_web_server/your_roygbiv_directory/

Note:

  • If you want your downloaded or generated data stored at specific location, please define the ROYGBIV_PATH environment variable.