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version 1.1 (96.4 MB) by Daniele Mascali
Visualize and print volumetric brain data


Updated 04 Oct 2021

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BrainSlicer is a MATLAB-based visualization tool for volumetric brain data. Its main purpose is to produce publication-level figures.

BrainSlicer main functionalities include:

  • possibility of overlaying multiple images with tunable opacity.
  • thresholding and clusterization of each layer
  • visualize colorbar for each desired layer
  • handy visualization of p-value maps as (1-p)
  • ~ 100 colormaps available (including FSL and brain colours maps)

BrainSlicer is composed of three main programs:

  • slicer.m - the main tool, visualizes and prints nifti images.
  • slicerCollage.m - combines several images produced by slicer.m in a single figure.
  • colormaps.m - shows all the available colormaps and their code for ease of selection.


BrainSlicer requires:

  • SPM
  • MATLAB version >= R2014b


SlicerDemo.m demostrates the major functionalities of the toolbox using common usage examples.

  • Figure showing a t-map and 1-p-map:  Example 2 
  • Figure showing the 10 networks from Smith et al. 2009 (PNAS):  Example 3 
  • Figure showing the 7 networks from Yeo et al. 2011 (J Neurophysiol) parcellated according to Schaefer et al 2018 (Cortex):  Example 3 

Cite As

Daniele Mascali (2022). BrainSlicer (, GitHub. Retrieved .

MATLAB Release Compatibility
Created with R2020a
Compatible with R2014b and later releases
Platform Compatibility
Windows macOS Linux

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To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.