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2d and 3d brain plots

version 1.6 (98.7 KB) by

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



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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Note: this version is no longer maintained.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:

Comments and Ratings (8)

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


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

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

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...


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

David Cahn

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.

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?




include link to github version


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


Fixed some documentation errors, added support for more formats.


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


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


Include file dependencies in the download.


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

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MATLAB 8.5 (R2015a)

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