fMRI-Volumetric-Renderer

A volumetric fMRI renderer for jupyter notebook. Built using WebGL.

This project presents a method for visualizing volumetric MRI and fMRI data based on a discrete raytracing algorithm and OpenGL. Data is pre-processed and then attached to the html template document, the renderer itself is written in html. This method presents a lightweight renderer that can be used to visualize fMRI data in the output of a jupyter notebook.

Interactive example: Here

Python Render Pipeline Usage

Get the package from the pip repository using the python pip command

pip install fMRI-Volumetric-Renderer

Basic usage involves nibabel to unpack a fmri volume into a tensor
From there you can manipulate the data or pass it raw into the renderer

import nibabel as nib
import numpy as np
from volume_plot_utils import plotter

#load an example nifti file
brainData = nib.load("data/sub-0x/func/subject-data-file.nii.gz")

#load the nifti data into a pytorch tensor
activationSequence = brainData.get_fdata().T

#use the displayVolume function to display the volumetric data in ipynb
plotter.displayVolume(activationSequence)

General HTML Template Usage

The example python shows usage with pytroch and nibabel but html displays can be created from a template by substituting keywords from the template file: see plotter.py for more information

Interactive example: Here