haozx2014 / slice_display

Slice Display is a MATLAB toolbox for visualizing fMRI data. It can make dual-coded images (simultaneous display of contrast estimate and unthreshold t-statistic maps) that show more and hide less.

Slice Display

Overview

Slice Display is a MATLAB toolbox for visualizing fMRI data. Besides standard fMRI displays, it can make dual-coded images (simultaneous display of contrast estimate and unthreshold t-statistic maps). Data visualizations can be entirely scripted, so that generating figures is easy and reproducible.

Typical visualization of fMRI data - thresholded t-map

Alternative visualization of fMRI data - dual-coded map

• Simultaneous display of effect size (color-coded) and unthresholded inferential statistics (opacity-coded)
• Contours distinguish statistically significant and non-significant voxels
• Show more and hide less, while allowing for spatial localization

Getting started

Requirements

• MATLAB R2015a or later
• MATLAB Statistics Toolbox
• SPM by the Wellcome Trust Centre for Neuroimaging at UCL
• Panel by Ben Mitch

Installation

You can either download the code as a ZIP file or you can clone the code:

To download the code:

1. Go to the Slice Display repository on GitHub.
2. Select 'Download ZIP' from the green 'Clone or download' button.

To clone the code, run the following command on the command line (require Git to be installed):

git clone https://github.com/bramzandbelt/slice_display.git

Usage

See the example scripts in the directory 'examples'.

Papers & preprints using Slice Display

• van Lieshout, L. L., Vandenbroucke, A. R., Müller, N. C., Cools, R., & de Lange, F. P. (2018). Induction and relief of curiosity elicit parietal and frontal activity. Journal of Neuroscience, 38(10), 2579-2588.
• Richter, D., Ekman, M., & de Lange, F. P. (2018). Suppressed sensory response to predictable object stimuli throughout the ventral visual stream. Journal of Neuroscience, 38(34), 7452-7461.
• Ai, H., Xin, Y., Luo, Y., Gu, R., & Xu, P. (2019). Volume of motor area predicts motor impulsivity. European Journal of Neuroscience.

Citation

If you intend to publish figures obtained with this code, cite it as follows:

• Zandbelt, Bram (2017): Slice Display. figshare. 10.6084/m9.figshare.4742866.

If you intend to publish figures using dual-coded design, also cite the following paper:

• Allen, E. A., Erhardt, E. B., & Calhoun, V. D. (2012). Data Visualization in the Neurosciences: Overcoming the Curse of Dimensionality. Neuron, 74(4), 603–608. https://doi.org/10.1016/j.neuron.2012.05.001

Colophon

Version

Version 0.1 - March 2017

Contact

E-mail: [email protected]

Acknowledgment

Slice Display was inspired by and builds on the slice overlay toolbox by Matthew Brett, available through SPM.

References

Allen, E. A., Erhardt, E. B., & Calhoun, V. D. (2012). Data Visualization in the Neurosciences: Overcoming the Curse of Dimensionality. Neuron, 74(4), 603–608. https://doi.org/10.1016/j.neuron.2012.05.001