OHBM Brainhack: Integrating niivue into html reports

[korbinian90]

Summary

This was an experiment to see if niivue can be easily included in the html output. The main issue identified is the CORS policy (security feature that disallows opening local files by javascript code).

Why it works on png / svg files
They are directly rendered by the browser and don't trigger the CORS policy, because no arbitrary javascript code execution can happen.

Why it doesn't work on NIfTI files with niivue
niivue is a javascript library and is not allowed to access local files, because of CORS security enforcing. To open files, they need to be served by a server with CORS headers.

Possible workarounds

• Open a python server that serves the files while creating the report only works while the notebook still is running (program that created the html file) Code that does this
• Create callable scripts (.sh / .bat) that run a local http server and host the local nifti files (python -m http.server). requires a local python and second user engagement. When the file is not available, this could also appear in the html as "To be able to see live rendered nifti image, run python -m http.server in the console in the folder of the html file" Code that works after running "python -m http.server"
• Embed the nifti file in the html as base64, which bloats the size of the html file, but only needs a simple click from the user perspective Code that doesn't work yet, probably niivue call needs to be fixed to url:-name.nii.gz- data:-base64-

[eurunuela]

When I built Rica, I managed to upload local files to generate the reports. I never had the bandwidth to add niivue but it still is one of my future goals. In case it's useful, you could have a look to see how I dealt with uploading the different files.

[korbinian90]

Yes, uploading and hosting files avoids the CORS restriction. The same for jupyter (notebook or book) since it is hosted.
In jupyter, I would suggest to use ipyniivue, which has a convenient interface for python.

[tsalo]

If we want to add more dependencies, then I think we need to prioritize the minimal installation option to maximize compatibility with tools that don't use these features (esp. fMRIPrep).