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Volumetric 3

version 1.0.05 (12.3 MB) by James Ryland
3D Volumetric fMRI visualization

2.2K Downloads

Updated 06 Mar 2020

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View Demo on Youtube Here:
https://youtu.be/l-8qO7uox_4
Brief Painting Tutorial:
https://youtu.be/SKra3QYvfG8

Summary:
Volumetric is a full application in Matlab designed to let you create and edit 3D visualizations of brain imaging data. Volumetric easily allows layering and displaying multiple channels of data. It features Volumetric rendering which allows for transparent solids that change color and consistency. You can make very simple and clean visualizations for publication or radically detailed and beautiful brain illustrations or anything in-between. It features a real time layer editor and a ray trace method for producing even higher quality images.
Volumetric only works with data files that have been properly co-registered to a shared space. This can be accomplished using common tools like AFNI and SPM. Typical co-regestration project fMRI coordinates to fMRI coordinates or anatomical coordinates to fMRI coordinates. For visualization purposes you want to project into the highest resolution space possible so you need to project from fMRI to Anatomical coordinates. A tutorial is provided using SPM to help people get accustomed to this work flow.

Volumetric can technically visualize and layer any volumetric data (3D voxel density data). This includes scalar fields, potentially 3D vector fields (if clever), simulation data, geo survey data, and many other domains. Anything that can be converted to a matlab 3D array can be loaded by Volumetric. However size and memory issues can occur depending on scale.
Here are some demo files uploaded to mathworks:
http://www.mathworks.com/matlabcentral/fileexchange/63083-volumetric-3-demo-redscull <- this is the icon at the top
http://www.mathworks.com/matlabcentral/fileexchange/63084-volumetric-3-demo-bluebrain

If you use volumetric for publication purposes please make mention of the Author and cite if possible. I did spend an inordinate amount of time building volumetric 1 2 and 3 so a little recognition would be lovely. I might put some youtube tutorials up at some point.
A lot of people have been asking about this, so I should probably just put it here:
-(Load) at the top of the layer editor loads in a pre-built vl3 visualization file
-(Load Color Source) in the layer editor load in a raw 3D matrix as either .mat or .img, and will allow you to apply a color and transparency mapping to your values.
-(Load Alpha Source) if enabled will allow you to load a 3D matrix for transparency values independently from color
- (The Colored and Grey bars) at the bottom of the layer editor are the color and transparency mappings from low to high. You can paint them by clicking on them, which will update the 3D visualization.
- I will make a YouTube video of the painting process. and link it here soon!

Works on:
Mac
PC
Linux
Bug Notes:
* Not intended as a toolbox: Recommend downloading as a zip instead and navigating to the Volumetric 3 directory to start
Volumetric. A toolbox version has been uploaded, but not tested....
* Realtime editor has a graphical glitch for Matlab 2016
* Raytrace works but is under development,
* Ray trace lighting is hard to use and unsupported

Author: James Ryland
Institution: The University of Texas at Dallas

Publications that can be cited if you use my software:
1. O’Toole, A. J., Natu, V., An, X., Rice, A., Ryland, J. & Phillips, P. J. (2014). The neural representation of faces and bodies in motion and at rest. NeuroImage. 91, 1-11. http://dx.doi.org/10.1016/j.neuroimage.2014.01.038.
2. Ryland, J. (2013). Volumetric Visualization Technique for Brain Imaging, 2013 International Joint Conference on
Neural Networks.

Cite As

James Ryland (2021). Volumetric 3 (https://www.mathworks.com/matlabcentral/fileexchange/59161-volumetric-3), MATLAB Central File Exchange. Retrieved .

MATLAB Release Compatibility
Created with R2013b
Compatible with R2012b to R2014b
Platform Compatibility
Windows macOS Linux
Acknowledgements

Inspired by: vol3d v2, DTI and Fiber Tracking

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