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Visualization tool for fMRI data-sets using Plotly Dash
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README.md

VoxelViz

Visualization tool for (f)MRI data-sets using Plotly Dash. Submitted to the TransIP VPS competition.

UPDATE: I won the competition! Thanks for TransIP/Tweakers for hosting this competition (and the 1st prize: a kick-ass gaming laptop and HTC Vive) -- this definitely motivated me to keep on developing this app!

To do

Couple of thing that I'd still like to implement and (relatively unimportant) bugfixes.

To fix:

  • Fix update timeseries when changing brainplot
  • Fix range of slice-scrolling (currently sometimes out of range)
  • Fix automatic range in heatmap (colors are now variable)
  • Fix location (and text-color) of model/voxel checkbox!
  • Fix darkgrey text on Hover-box

To implement:

  • Refactor to make standalone app!
  • Add option to load in own data (with dcc.Load component)
  • Add option to show separate regressors (not only model fit)
  • Option to toggle between timeseries and frequency view (nice to show effect of e.g. highpass filter)
  • Add download script to download data to check examples (teaching/showcase) locally

Intro

This tool was originally developed for the TransIP VPS competition ("come up with an original idea for a virtual private server"), but mainly because I was looking for an excuse to mess around with the new Plotly Dash framework. The app turned out better than I expected and I think I'll try to convert it into an open-source package for everyone to use. That is, I'll rewrite it such that any neuroimaging researcher (or teacher! more about that later) with a proper dataset can use VoxelViz to show/demonstrate it.

Usage

As of now, VoxelViz can be used in two ways, which correspond to the two apps in this repository (the one in the usecase folder and the one in the teaching folder).

Showcase results

First, it can be used to interactively visualize results from (group-level) fMRI analyses. Or, in layman terms: show pretty brain pictures. In the usecase folder, the app.py file runs an app that shows the results from my fMRI study (freely accessible!) about the representation of emotion in the brain. VoxelViz visualizes the brain images corresponding to the different analyses we did (left panel of the app), which can be interactively manipulated by, for example, adjusting the statistical threshold, orientation (X, Y, Z), and the current "slice" (specific 2D view; changing this is like "scrolling" through the brain image).

Additionally, VoxelViz interactively visualizes the "timeseries" from the voxel (3D cube, which represents the unit of measurement) that you hover over in the brain image from the app's left panel. So, the right panel (timeseries plot) updates according to where your cursor is in the app's right panel - cool huh?

Teaching neuroimaging

Next to the "showcase" use, I think this app could be quite helpful in a teaching context. It happens to be that I myself teach two "neuroimaging" (analysis of brain-data) courses at the University of Amsterdam, and I struggly to explain "dry" (often statistical) concepts during my lectures and computer labs. Of course, I try to make my lectures more "lively" by including a lot of brain images, but 2D representations just don't do the trick. How cool would it be to show students "boring" things, like the effect of a high-pass filter on fMRI analyses, interactively in a web-app? Well, the folder teaching of this repository contains an app for just that! It shows the results (brain images) from different preprocessing pipelines. This way, you can check out (or show students) what happens to the brain images when you apply a high-pass filter (or not!) or when you (spatially) smooth your data. This should be especially clear from the timeseries plot in the right panel!

Features

I've alluded to some of the features in the previous section already, but here I'll describe them in more detail.

Show different datasets/results

When you start the app, you'll see a dropdown menu in the top left corner of the brain image plot. In the showcase example app, this dropdown menu contains the "contrasts" (results) from different analyses, which are referred to by keywords such as "action", "interoception", "action>interoception", etc. (These results refer to analyes which tested how the brain activates in response to action-oriented emotional states, interoception-oriented emotional states, and the difference between action and interoception states, respectively.) Changing the "contrast" will update both the brain plot and the timeseries plot!

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Viewing/scrolling options

The brain is of course a 3D dimensional object that is, here, visualized in 2D. I've included two options to configure which part (and in which orientation) you're viewing the brain image. Next to the "contrasts" dropdown menu, you can choose whether you want to view the brain in a saggital orientation (from the side; "X"), coronal orientation (from the front; "Y"), or axial orientation (from the top; "Z"). Next to the "X/Y/Z" option, there is a slides that allows you "scroll" through the brain.

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Adjust the (statistical) threshold

Usually, results from (f)MRI analyses are thresholded, to remove insignificant (de)activations. Therefore, the results are by default thresholded at abs(Z) > 2.3. But sometimes its informative to check out the unthresholded results, so VoxelViz contains a slides to adjust the threshold! Adjusting the threshold automatically updates the brain plot (higher thresholds should show less red/blue and vice versa).

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Visualize underlying timeseries

In the right panel of the app, there is a "timeseries" plot that shows the underlying signal of the highlighted voxel (3D equivalent of pixel) in the brain plot. In other words, if you hover over a voxel in the brain plot, the timeseries plot will automatically show the underlying signal of that voxel.

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Visualize model fit

The "results" in the left panel (the brain plot) are derived from models fit to the timeseries data in the right panel. By clicking on the "Model" checkbox above the right plot, you can visualize the model fit to the data, which again updates when you change the position of your cursor. This is especially helpful in a teaching context when you want to show students the effect of preprocessing options (such as filtering, confound regression, etc.) on your model fit!

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See for yourself!

VoxelViz runs as a standalone app on a VPS X8 BladeVPS from TransIP, which can be viewed at teaching.lukas-snoek.com and showcase.lukas-snoek.com.

If you want to mess around with the app yourself with your own data, you can clone this repo! First, you need to install the dependencies, which you can do through:

$ pip install -r requirements.txt

Then, put your own data in the usecase or teaching folder (and rename the folder if you want), change the config.json file, and run:

$ python app.py

Now, go to http://localhost:8050 in your browser to view and use the app!

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