K-Particles: A visual journey into the heart of magnetic resonance imaging

[ofgulban]

Authors

Omer Faruk Gulban faruk.gulban@maastrichtuniversity.nl
Kenshu Koiso k.koiso@maastrichtuniversity.nl
Thomas Maullin-Sapey thomas.maullin-sapey@bdi.ox.ac.uk
Jeff Mentch jsmentch@mit.edu
Alessandra Pizzuti a.pizzuti@maastrichtuniversity.nl
Fernanda Ponce | <TO_BE_FILLED_IN_LATER_WE_COULD_NOT_REACH_HER>
Kevin R. Sitek kevin.sitek@northwestern.edu
Paul A. Taylor paul.taylor@nih.gov

Summary

Introduction

The primary objective of this project is to leverage particle animations to provide insights into the journey of traveling and sampling the k-space. By generating captivating visualizations, we aim to demystify the concept of k-space and the role it plays in magnetic resonance imaging (MRI), engaging both the scientific community and the general public in a delightful exploration of this fundamental aspect of imaging. This project builds on our previous Brainhack experiences that focused on generating 3D geodesic distance computation animations [CITE Brainhack2021] and particle simulation based brain explosions [CITE Brainhack2022].

Methods

Our methodology is as follows. First, we start from a 2D brain image (e.g. selecting a slice from a 3D anatomical MRI data [CITE Nibabel, Numpy, Scipy]). Then, we take its Fourier Transform and subsequently perform masking (or magnitude scaling) operations on k-space data [CITE Bernstein2004], the transform. We then create simultaneous visualizations of the k-space magnitude and corresponding image-space magnitude data. Note that the masking of k-space data is where the participants of this project exercised their creativity, by setting up various initial conditions and a set of rules to animate the mask data. In the final step, animated frames are compiled into movies to inform (and entertain). The scripts we have used to program these steps are available at: https://github.com/ofgulban/k_particles . Note that, we have also included several animations where no brain images were used, but instead, we generated k-space data directly in k-space to guide the unfamiliar participants with the concepts (see Figure 1, Panel A).

Results

As a result of this hackathon project, a compilation of our progress (Figure 1, Panel B) can be seen at https://youtu.be/_5ZDctWv5X4 as a video. Some of the highlights are:

1. Audiovisualizer that maps audio features (e.g. amplitude) to k-space mask diameters
2. Game of life [CITE Gardner1970] simulation in k-space with Hermitian symmetry.
3. Pacman moving in k-space is implemented as a series of radial sector masks.
4. Semi-random initialization of particle positions and semi-randomly reassigned velocities that look like an emerging butterfly.
5. Randomized game of life initialization with vanishing trails of the previous simulation steps that look like stars, clouds, and comets orbiting frequency bands in k-space.
6. Semi-random initialization of particle positions and velocities that look like explosions.
7. Predetermined initialization of particle positions (e.g. at the center) and semi-randomized velocities that look like fireworks.
8. Dancing text animations where the positions of text pixels are manipulated by wave functions.
9. Picture based (e.g. cropped faces of the authors) moving within the k space where each pixel’s grayscale value is mapped onto a mask coefficient between 0-1.

Our future efforts will involve sophisticating the k-space simulations to generate more entertaining and educational content. For instance, instead of only visualizing the magnitude images, we can generate four panel animations showing real and imaginary (or magnitude and phase) components of the data.

Figure Caption

Figure 1: Our compilation of k-space animations generated during the brainhack can be seen at https://youtu.be/XS0LEQExGU8?si=I5Zufp3AcCbdhYIR .

References (Bibtex)

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[anibalsolon]

That's great, thank you @ofgulban

May I download the video from youtube and add it to Google Drive? We will add it to OSF, so to have a DOI with all the material.

[ofgulban]

@anibalsolon thanks! Yes of course, please feel free to download the video. If there are any issues let me know.

[ufangYang]

Hi @ofgulban We are currently compiling author information for our upcoming proceeding paper. Could you please take a moment to fill out your team member's details using the form provided here: https://forms.gle/XB4EKospj1PqkVBi7? Cheers!

[ofgulban]

@ufangYang , done thank you! Ah I just noticed that I should do it for every member. Will do!

[ofgulban]

Ok fully completed now, thanks again :)

[ufangYang]

@ofgulban thanks a bunch!