View License

Download apps, toolboxes, and other File Exchange content using Add-On Explorer in MATLAB.

» Watch video

Highlights from
2d and 3d brain plots

5.0 | 1 rating Rate this file 19 Downloads (last 30 days) File Size: 98.7 KB File ID: #36139 Version: 1.6
image thumbnail

2d and 3d brain plots



11 Apr 2012 (Updated )

Quickly and easily create 2d and 3d plots of fMRI data.

| Watch this File

File Information

Industry standard brain plotting programs are great for producing publication-quality images of brain data. However, these tools are often very slow. This suite of tools provides a means of quickly generating 2- or 3-dimensional plots of fMRI data that can be manipulated (e.g. rotated, modified) in real time.
Although these tools may be used to produce publication-quality figures, the focus here is on speed and ease of use. These tools are intended to be used for quickly exploring and examining fMRI data, debugging fMRI analyses, etc.
Note: this version is no longer maintained. Instead see:


Plot A 3 D Array Using Patch, Get Tight Subplot Handles, Slices, and Sane P Color(Varargin) inspired this file.

MATLAB release MATLAB 8.5 (R2015a)
MATLAB Search Path
Other requirements This file depends on: sanePColor (35601), getTightSubplotHandles (35435), slices (35436), and PATCH_3Darray (28497). These files are included in the download.
Tags for This File   Please login to tag files.
Please login to add a comment or rating.
Comments and Ratings (8)
09 Mar 2016 mima zebouchi

well i need a programme matlab for the extraction of the brain tissu

Comment only
07 May 2015 tahoorasf

how we can run plot_brain2d and 3d?if possible put one example for them.

Comment only
01 May 2015 luca benedettini

I want to thank you, your work is awsome and helped me a lot during my thesis work.
I wrote one versione of meta_select_voxels function before the correction. The toolbox seems to work well.
I would be very happy to share it with you. I would like to have the opinion of a much more experienced than me.
Best greetings Luca Benedettini

Comment only
01 May 2015 Jeremy Manning

Hi Luca,

Sorry about those missing files! I've updated the toolbox to include the missing files. You should see the new version appear shortly...


Comment only
24 Apr 2015 luca benedettini

i find one problem in this tools. In the mat_to_cmu.m function used to convert images in matrix format into CMU format. In this function is used meta_select_voxels function, but there isn't in the toolbax.
Thanks for helping

Comment only
30 Jul 2013 David Cahn

29 Jul 2013 Jeremy Manning

Hi David,

I would be happy to help. Can you please either describe your data in more detail or send me an example that triggers this error?

Note that if you set erode_layers too large, you will encounter an error, since only as many layers as exist may be stripped off of the brain image.

Comment only
26 Jul 2013 David Cahn


I downloaded your code, but when I run brain_plot3d_alt, it prints a 2D image instead of a 3D image. I'm using the standard MNI brain...

Also, every time I try to put in an input for erode_layers the code throws an error. What's going wrong?


Comment only
11 Apr 2012 1.1

updated documentation in plot_brain3d -- erode_layers parameter was incorrectly described in previous version.

25 Apr 2012 1.2

Include file dependencies in the download.

22 Feb 2013 1.3

added two new functions that plot from 3d matrices (tensors) rather than requiring the meta matrix.

11 Dec 2013 1.4

I have made a number of changes with this update that are intended to make the plotting functions easier to use.

12 Dec 2013 1.5

Fixed some documentation errors, added support for more formats.

01 May 2015 1.6

I've added two missing files and have included minor updates to several functions.

17 Jan 2017 1.6

include link to github version

Contact us